scholarly journals Environmental factors shape the epiphytic bacterial communities of Gracilariopsis lemaneiformis

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pengbing Pei ◽  
Muhammad Aslam ◽  
Hong Du ◽  
Honghao Liang ◽  
Hui Wang ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Community Composition ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Inorganic Nitrogen ◽  
Critical Role ◽  
Gracilariopsis Lemaneiformis ◽  
Rrna Gene ◽  
Epiphytic Bacteria ◽  
Geographic Locations

AbstractMacroalgae host various symbionts on their surface, which play a critical role in their growth and development processes. However, there is still incomplete understanding of this epiphytic bacteria-host algae interactions. This study comprehensively analysed variation of the epiphytic bacterial communities (EBC) composition of red macroalga Gracilariopsis lemaneiformis at different geographic locations and environmental factors (i.e., nitrogen and phosphorus), which shape the EBC composition of G. lemaneiformis. The composition and structure of EBC were characterized using high throughput sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The results revealed that epiphytic bacteria varied significantly among three different geographic locations in China, i.e., Nan’ao Island (NA), Lianjiang County (LJ), and Nanri Island (NR). Redundancy analysis (RDA) showed that the relative abundance of Bacteroidetes, Firmicutes, Verrucomicrobia, and Epsilonbacteraeota at NR were strongly positively correlated with total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NO3-N), and dissolved inorganic nitrogen (DIN), but negatively correlated with nitrite nitrogen (NO2-N). The relative abundance of Cyanobacteria at NA and LJ were strongly positively correlated with NO2-N, but negatively correlated with TN, TP, NO3-N, and DIN. Besides, the Mantel test results indicated that the EBC composition was significantly correlated with these environmental factors, which was also confirmed by Spearman correlation analysis. Thus, environmental factors such as NO3-N and DIN play a key role in the community composition of epiphytic bacteria on G. lemaneiformis. This study provides important baseline knowledge on the community composition of epiphytic bacteria on G. lemaneiformis and shows correlation between different epiphytic bacteria and their surrounding environmental factors.

scholarly journals Environmental Factors Shape the Epiphytic Bacterial Communities of Gracilariopsis Lemaneiformis

2021 ◽  
Author(s):  
Pengbing Pei ◽  
Hong Du ◽  
Muhammad Aslam ◽  
Honghao Liang ◽  
Hui Wang ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Inorganic Nitrogen ◽  
Pearson Correlation ◽  
Critical Role ◽  
Gracilariopsis Lemaneiformis ◽  
Rrna Gene ◽  
Epiphytic Bacteria

Abstract Macroalgae host variety of symbionts on their surface which play critical role in their growth and development processes. Nevertheless, the complete understanding of this interaction of epiphytic bacteria and host algae is still in its infancy. This study comprehensively analyses epiphytic bacterial communities composition of red macroalga Gracilariopsis lemaneiformis and environmental factors such as nitrogen and phosphorus which shape the composition of epiphytic bacterial communities of G. lemaneiformis and variation of epiphytic bacterial communities composition at different geographical location. The composition and structure of epiphytic bacterial communities were characterized using high throughput sequencing data of the V3-V4 hypervariable region of 16S rRNA gene amplicon sequencing. The epiphytic bacterial communities composition data revealed that epiphytic bacteria varied significantly among three different geographic locations i) Nan’ao Island (NA) (ii) Lianjiang County (LJ) and iii) Nanri Island (NR) in China. Redundancy analysis (RDA) showed that the relative abundance of Bacteroidetes, Firmicutes, Verrucomicrobia and Epsilonbacteraeota at NR were strongly positively correlated with total nitrogen (TN), total phosphorus (TP), nitrate nitrogen (NO3-N), and dissolved inorganic nitrogen (DIN), whereas negatively correlated with nitrite nitrogen (NO2-N). In addition, the relative abundance of cyanobacteria at NA and LJ were strongly positively correlated with NO2-N, whereas negatively correlated with TN, TP, NO3-N, and DIN. Furthermore, the results of Mantel test indicated that the epiphytic bacterial communities composition is significantly correlated with these environmental factors, which are also proved by Pearson correlation analysis. In conclusion, it is proposed that environmental factors such as NO3-N and DIN play key role in the communities composition of epiphytic bacteria in G. lemaneiformis. Our study provides important baseline knowledge for the communities composition of epiphytic bacteria in G. lemaneiformis and their correlation among themselves as well as with their surrounding environmental factors.

scholarly journals A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1658
Author(s):  
Jan C. Plaizier ◽  
Anne-Mette Danscher ◽  
Paula A. Azevedo ◽  
Hooman Derakhshani ◽  
Pia H. Andersen ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Dry Matter ◽  
Control Diet ◽  
Rrna Gene ◽  
Ruminal Acidosis ◽  
Clustering Patterns ◽  
The 16S Rrna Gene ◽  
Distal Jejunum

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

scholarly journals Rumen Sampling Methods Bias Bacterial Communities Observed

2021 ◽  
Author(s):  
Jill V. Hagey ◽  
Maia Laabs ◽  
Elizabeth A. Maga ◽  
Edward J. DePeters
Keyword(s):  
Relative Abundance ◽  
Critical Role ◽  
Cost Effective ◽  
Feed Additives ◽  
Rrna Gene ◽  
Stomach Tube ◽  
Fecal Samples ◽  
Rumen Microbes ◽  
Lower Abundance ◽  
The Family

AbstractThe rumen is a complex ecosystem that plays a critical role in our efforts to improve feed efficiency of cattle and reduce their environmental impacts. Sequencing of the 16S rRNA gene provides a powerful tool to survey shifts in the microbial community in response to feed additives and dietary changes. Oral stomach tubing a cow for a rumen sample is a rapid, cost-effective alternative to rumen cannulation for acquiring rumen samples. In this study, we determined how sampling method, as well as type of sample collected (liquid vs solid), bias the microbial populations observed. The abundance of major archaeal populations was not different at the family level in samples acquired via rumen cannula or stomach tube. Liquid samples were enriched for the order WCHB1-41 (phylum Kiritimatiellaeota) as well as the family Prevotellaceae and had significantly lower abundance of Lachnospiraceae compared with grab samples from the rumen cannula. Solid samples most closely resembled the grab samples; therefore, inclusion of particulate matter is important for an accurate representation of the rumen microbes. Stomach tube samples were the most variable and were most representative of the liquid phase. In comparison with a grab sample, stomach tube samples had significantly lower abundance of Lachnospiraceae, Fibrobacter and Treponema. Fecal samples did not reflect the community composition of the rumen, as fecal samples had significantly higher relative abundance of Ruminococcaceae and significantly lower relative abundance of Lachnospiraceae compared with samples from the rumen.

scholarly journals Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum

2019 ◽  
Vol 96 (1) ◽  
Author(s):  
Stefanie P Glaeser ◽  
Iulian Gabur ◽  
Hossein Haghighi ◽  
Jens-Ole Bartz ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Oilseed Rape ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Quantitative Resistance ◽  
Bacterial Community Composition ◽  
Phylogenetic Group ◽  
Rrna Gene ◽  
Host Genotype ◽  
Brassica Napus L ◽  
Verticillium Longisporum

ABSTRACT Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.

scholarly journals Plant Growth Promotion Potential Is Equally Represented in Diverse Grapevine Root-Associated Bacterial Communities from Different Biopedoclimatic Environments

2013 ◽  
Vol 2013 ◽  
pp. 1-17 ◽  
Author(s):  
Ramona Marasco ◽  
Eleonora Rolli ◽  
Marco Fusi ◽  
Ameur Cherif ◽  
Ayman Abou-Hadid ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Plant Growth ◽  
Bacterial Communities ◽  
Growth Promotion ◽  
Rrna Gene ◽  
Similar Distribution ◽  
Bacterial Assemblage ◽  
Pgp Traits ◽  
Associated Bacteria

Plant-associated bacteria provide important services to host plants. Environmental factors such as cultivar type and pedoclimatic conditions contribute to shape their diversity. However, whether these environmental factors may influence the plant growth promoting (PGP) potential of the root-associated bacteria is not widely understood. To address this issue, the diversity and PGP potential of the bacterial assemblage associated with the grapevine root system of different cultivars in three Mediterranean environments along a macrotransect identifying an aridity gradient were assessed by culture-dependent and independent approaches. According to 16S rRNA gene PCR-DGGE, the structure of endosphere and rhizosphere bacterial communities was highly diverse (P=0.03) and was associated with a cultivar/latitudinal/climatic effect. Despite being diverse, the bacterial communities associated with Egyptian grapevines shared a higher similarity with the Tunisian grapevines than those cultivated in North Italy. A similar distribution, according to the cultivar/latitude/aridity gradients, was observed for the cultivable bacteria. Many isolates (23%) presentedin vitromultiple stress resistance capabilities and PGP activities, the most frequent being auxin synthesis (82%), insoluble phosphate solubilisation (61%), and ammonia production (70%). The comparable numbers and types of potential PGP traits among the three different environmental settings indicate a strong functional homeostasis of beneficial bacteria associated with grape root.

scholarly journals Changes of Bacterial Communities in Response to Prolonged Hydrodynamic Disturbances in the Eutrophic Water-Sediment Systems

2019 ◽  
Vol 16 (20) ◽  
pp. 3868
Author(s):  
Haomiao Cheng ◽  
Ling Cheng ◽  
Liang Wang ◽  
Tengyi Zhu ◽  
Wei Cai ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Bacterial Communities ◽  
16S Rrna Gene Sequencing ◽  
Aquatic Environments ◽  
Rrna Gene ◽  
Evolutionary Trend ◽  
Ecological Evaluation ◽  
Eutrophic Water ◽  
Rrna Gene Sequencing ◽  
Opposite Tendency

The effects of hydrodynamic disturbances on the bacterial communities in eutrophic aquatic environments remain poorly understood, despite their importance to ecological evaluation and remediation. This study investigated the evolution of bacterial communities in the water–sediment systems under the influence of three typical velocity conditions with the timescale of 5 weeks. The results demonstrated that higher bacterial diversity and notable differences were detected in sediment compared to water using the 16S rRNA gene sequencing. The phyla Firmicutes and γ-Proteobacteria survived better in both water and sediment under stronger water disturbances. Their relative abundance peaked at 36.0%, 33.2% in water and 38.0%, 43.6% in sediment, respectively, while the phylum Actinobacteria in water had the opposite tendency. Its relative abundance grew rapidly in static control (SC) and peaked at 44.8%, and it almost disappeared in disturbance conditions. These phenomena were caused by the proliferation of genus Exiguobacterium (belonging to Firmicutes), Citrobacter, Acinetobacter, Pseudomonas (belonging to γ-Proteobacteria), and hgcI_clade (belonging to Actinobacteria). The nonmetric multidimensional scaling (NMDS) and Venn analysis also revealed significantly different evolutionary trend in the three water-sediment systems. It was most likely caused by the changes of geochemical characteristics (dissolved oxygen (DO) and nutrients). This kind of study can provide helpful information for ecological assessment and remediation strategy in eutrophic aquatic environments.

scholarly journals Biofilm thickness matters: Deterministic assembly of different functions and communities in nitrifying biofilms

2018 ◽  
Author(s):  
Carolina Suarez ◽  
Maria Piculell ◽  
Oskar Modin ◽  
Silke Langenheder ◽  
Frank Persson ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Environmental Factors ◽  
Community Composition ◽  
Community Assembly ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Strong Impact ◽  
Biotechnological Applications ◽  
Biofilm Thickness ◽  
Microbial Biofilms

ABSTRACTMicrobial biofilms are important in natural ecosystems and in biotechnological applications. Biofilm architecture influences organisms’ spatial positions, who their neighbors are, and redox gradients, which in turn determine functions. We ask if and how biofilm thickness influences community composition, architecture and functions. But biofilm thickness cannot easily be isolated from external environmental factors. We designed a metacommunity system in a wastewater treatment plant, where either 50 or 400 µm thick nitrifying biofilms were grown simultaneously on biofilm carriers in the same reactor. Model simulations showed that the 50 µm biofilms could be fully oxygenated whereas the 400 µm biofilms contained anaerobic zones. The 50 and 400 µm biofilms developed significantly different communities. due to deterministic factors were stronger than homogenizing dispersal forces in the reactor, despite the fact that biofilms experienced the same history and external conditions. Relative abundance of aerobic nitrifiers was higher in the 50 µm biofilms, while anaerobic ammonium oxidizers were more abundant in the 400 µm biofilms. However, turnover was larger than the nestedness component of between-group beta-diversity, i.e. the 50 µm biofilm was not just a subset of the thicker 400 µm biofilm with reduced taxa richness. Furthermore, the communities had different nitrogen transformation rates. The study shows that biofilm thickness has a strong impact on community composition and ecosystem function, which has implications for biotechnological applications, and for our general understanding of biofilms.IMPORTANCEMicroorganisms colonize all surfaces in water and form biofilms. Diffusion limitations form steep gradients of energy and nutrient sources from the water phase into the deeper biofilm parts, influencing community composition through the biofilm. Thickness of the biofilm will affect diffusion gradients, and is therefore presumably important for biofilm composition. Since environmental factors determine thickness, studies of how thickness influences biofilm functions and community assembly, have been difficult to perform. We studied biofilms for wastewater treatment with fixed thicknesses of 50 and 400 µm during otherwise similar conditions and history. Despite growing in the same wastewater reactor, 16S rRNA gene sequencing and confocal microscopy showed the formation of two different communities, performing different ecosystem functions. Using statistical methods, we show for the first time, how biofilm thickness influences community assembly. The results help our understanding of the ecology of microbial biofilms, and in designing engineered systems based on ecological principles.

scholarly journals Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250675
Author(s):  
Xiang Zheng ◽  
Qidi Zhu ◽  
Zhijun Zhou ◽  
Fangtong Wu ◽  
Lixuan Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Structure ◽  
Feeding Habits ◽  
Bacterial Community Composition ◽  
Critical Role ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Insect Gut

Insect microbial symbioses play a critical role in insect lifecycle, and insect gut microbiome could be influenced by many factors. Studies have shown that host diet and taxonomy have a strong influence on insect gut microbial community. In this study, we performed sequencing of V3-V4 region of 16S rRNA gene to compare the composition and diversity of 12 Ensifera from 6 provinces of China. Moreover, the influences of feeding habits and taxonomic status of insects on their gut bacterial community were evaluated, which might provide reference for further application research. The results showed that Proteobacteria (45.66%), Firmicutes (34.25%) and Cyanobacteria (7.7%) were the predominant bacterial phyla in Ensifera. Moreover, the gut bacterial community composition of samples with different feeding habits was significantly different, which was irrespective of their taxa. The highest diversity of gut bacteria was found in the omnivorous Ensifera. Furthermore, common and unique bacteria with biomarkers were found based on the dietary characteristics of the samples. However, the bacterial community structure of the Ensifera samples was significantly different from that of Caelifera. Therefore, we concluded that feeding habits and taxonomic status jointly affect the gut bacterial community composition of the samples from Orthoptera. However, the influence of feeding habit dominates when taxonomy category below the suborder level. In addition, the dominant, common and unique bacterial community structure could be used to predict the contrastic feeding habits of insects belonging to Ensifera.

scholarly journals The leaf bacterial microbiota of female and male kiwifruit plants in distinct seasons: assessing the impact of Pseudomonas syringae pv. actinidiae

2021 ◽  
Author(s):  
Aitana Ares ◽  
Joana Pereira ◽  
Eva Garcia ◽  
Joana Costa ◽  
Igor Tiago
Keyword(s):  
Bacterial Community ◽  
Pseudomonas Syringae ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Defense Mechanisms ◽  
Abiotic Factors ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Sequencing Platform ◽  
The Impact

The pandemic Pseudomonas syringae pv. actinidiae (Psa) has been compromising the production of the kiwifruit industry in major producing countries. Abiotic factors and plant gender are known to influence the disease outcome. To better understand their impact, we have determined the diversity of the leafs bacterial communities using the V5-V6 region of the 16S rRNA gene amplicon on the Illumina MiSeq sequencing platform. Healthy and diseased female and male kiwifruit plants were analyzed in two consecutive seasons: spring and autumn. This work describes whether the season, plant gender and the presence of Psa can affect the leaves bacterial community. Fifty bacterial operational taxonomic units (OTUs) were identified and assigned to five phyla distributed by 14 different families and 23 genera. The leaves of healthy female and male kiwi plants share most of the identified bacterial populations, that undergoes major seasonal changes. In both cases a substantial increase of the relative abundance of genus Methylobacterium is observed in autumn. The presence of Psa induced profound changes on leaves bacterial communities structure translated into a reduction in the relative abundance of previously dominant genera that had been found in healthy plants, namely Hymenobacter, Sphingomonas and Massilia. The impact of Psa was less pronounced in the bacterial community structure of male plants in both seasons. Some of the naturally occurring genera have the potential to act as an antagonist or as enhancers of the defense mechanisms paving the way for environmentally friendly and sustainable disease control.

244 Fertility Outcomes Associated with Reproductive Tract Cytokines and Microbiota in Postpartum Beef Cows

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 128-129
Author(s):  
Rebecca K Poole ◽  
Taylor B Ault-Seay ◽  
Rebecca R Payton ◽  
Phillip R Myer ◽  
Andrea S Lear ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Transforming Growth Factor Beta ◽  
Bacterial Communities ◽  
Reproductive Tract ◽  
Transforming Growth Factor ◽  
Pearson Correlation ◽  
Transrectal Ultrasound ◽  
Beef Cows ◽  
Rrna Gene ◽  
Concentration Data

Abstract Local immune activity in the reproductive tract is crucial in the response to uterine diseases, normal reproductive functions, and establishing pregnancy. Few studies have evaluated the influence of the local immune environment of the reproductive tract on fertility outcomes. The objectives were to 1) evaluate reproductive cytokine concentrations in postpartum cows undergoing estrus synchronization followed by timed artificial insemination (TAI) and 2) correlate reproductive bacterial communities with cytokine concentrations. Angus cows (n = 20) were subjected to a 7-Day Co-Synch protocol with pre-synchronization beginning 21 days prior (d -21) to TAI (d 0). Uterine and vaginal flushes were collected on d -21 and -2. Pregnancy was determined by transrectal ultrasound on d 30. Bacterial community profiling and analyses were conducted targeting the V1 to V3 hypervariable regions of the 16S rRNA gene. Cytokine concentrations for interleukin (IL)-1b, IL-6, IL-10, and transforming growth factor beta (TGF-β) were determined by commercial ELISA kits. Concentration data were analyzed using PROC MIXED and correlations using Pearson correlation in SAS. No differences were detected in vaginal samples (P >0.05). No differences in IL-10 or IL-1b concentrations were detected in uterine samples (P >0.05). Uterine TGF-β concentrations were greater in resulting pregnant than non-pregnant cows (44.0 ± 13.4 pg/mL vs 14.7 ± 4.9 pg/mL; P = 0.05). Uterine TGF-β was negatively correlated with the relative abundance of genera Treponema (r = -0.668; P = 0.05) in resulting non-pregnant cows on d -21. Uterine IL-6 concentrations were greater in resulting non-pregnant than pregnant cows (198.7 ± 21.8 pg/mL vs 144.3 ± 16.1 pg/mL; P = 0.05). Uterine IL-6 and the relative abundance of genera Butyrivibrio were positively correlated (r = 0.742; P = 0.02) in resulting non-pregnant cows on d -21. These results suggest possible relationships between uterine bacterial communities and cytokines prior to TAI that may ultimately affect fertility outcomes in beef cattle.

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