scholarly journals Dietary Fiber Influences Bacterial Community Assembly Processes in the Gut Microbiota of Durco × Bamei Crossbred Pig

2021 ◽  
Vol 12 ◽  
Author(s):  
Xianjiang Tang ◽  
Liangzhi Zhang ◽  
Chao Fan ◽  
Lei Wang ◽  
Haibo Fu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Dietary Fiber ◽  
Community Assembly ◽  
Cecal Content ◽  
High Fiber ◽  
Β Diversity ◽  
Composition And Structure ◽  
Α Diversity ◽  
Deterministic Processes ◽  
Crossbred Pigs

Several studies have shown that dietary fiber can significantly alter the composition and structure of the gut bacterial community in humans and mammals. However, few researches have been conducted on the dynamics of the bacterial community assembly across different graded levels of dietary fiber in different gut regions. To address this, 24 Durco × Bamei crossbred pigs were randomly assigned to four experimental chows comprising graded levels of dietary fiber. Results showed that the α-and β-diversity of the bacterial community was significantly different between the cecum and the jejunum. Adding fiber to the chow significantly increased the α-diversity of the bacterial community in the jejunum and cecum, while the β-diversity decreased. The complexity of the bacterial network increased with the increase of dietary fiber in jejunal content samples, while it decreased in cecal content samples. Furthermore, we found that stochastic processes governed the bacterial community assembly of low and medium dietary fiber groups of jejunal content samples, while deterministic processes dominated the high fiber group. In addition, deterministic processes dominated all cecal content samples. Taken together, the variation of gut community composition and structure in response to dietary fiber was distinct in different gut regions, and the dynamics of bacterial community assembly across the graded levels of dietary fiber in different gut regions was also distinct. These findings enhanced our knowledge on the bacterial community assembly processes in gut ecosystems of livestock.

scholarly journals Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Lu Luan ◽  
Chao Liang ◽  
Lijun Chen ◽  
Haotian Wang ◽  
Qinsong Xu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Assembly ◽  
Carbon Metabolism ◽  
Structural Equation ◽  
Equation Modeling ◽  
Deep Soil ◽  
Deterministic Processes ◽  
Stochastic Dispersal ◽  
Microbial Community Assembly

ABSTRACT Soil microbial community assembly is crucial for understanding the mechanisms of microbial communities that regulate ecosystem-level functioning. The relative contributions of stochastic and deterministic processes to microbial community assembly remain poorly defined, and major questions exist concerning the soil organic carbon (SOC) dynamics of microbial community assembly in deep soil. Here, the bacterial community assembly processes were explored across five soil profile depths (up to 80 cm) during a 15-year field experiment involving four fertilization regimes. We found that the bacterial community assembly was initially governed by deterministic selection in topsoil but was progressively structured by increasing stochastic dispersal with depth. The migration rate (m) and β-null deviation pattern supported the hypothesis of a relatively greater influence of dispersal in deep soil, which was correlated with bacterial community assembly by stochastic processes. These changes in the entire community assembly reflected consistent assembly processes of the two most dominant phyla, Acidobacteria and Chloroflexi. Structural equation modeling showed that soil features (pH and total phosphorus) and bacterial interactions (competition and network complexity) were significantly related to bacterial community assembly in the 0-to-10-cm and 10-to-20-cm layers. Partial Mantel tests, structural equation modeling, and random forest modeling consistently indicated a strong and significant correlation between bacterial community assemblages and SOC dynamics, implying that bacterial assembly processes would potentially suppress SOC metabolism and mineralization when the contributions of stochastic dispersal to communities increased in deeper layers. Our results have important implications for integrating bacterial community assembly processes into the predictions of SOC dynamics. IMPORTANCE We have provided a framework to better understand the mechanisms governing the balance between stochastic and deterministic processes and to integrate the shifts in community assembly processes with microbial carbon metabolism. Our study reinforced that environmental filtering and bacterial cooccurrence patterns influence the stochastic/deterministic continuum of soil bacterial community assembly and that stochasticity may act through deeper soil layers to influence carbon metabolism. Delineating theoretically the potential linkages between community assembly and SOC dynamics across a broad range of microbial systems represents an interesting topic for future research.

scholarly journals Microbiome assembly predictably shapes diversity across a range of disturbance frequencies

2021 ◽  
Author(s):  
Ezequiel Santillan ◽  
Stefan Wuertz
Keyword(s):  
Temporal Dynamics ◽  
Ecological Communities ◽  
Β Diversity ◽  
Α Diversity ◽  
Deterministic Processes ◽  
Specialized Function ◽  
Successional Stages ◽  
And Function ◽  
Microbiome Assembly

Diversity is frequently linked to the functional stability of ecological communities. However, its association with assembly mechanisms remains largely unknown, particularly under fluctuating disturbances. Here, we subjected complex bacterial communities in bioreactor microcosms to different frequencies of organic loading shocks, tracking temporal dynamics in their assembly, structure and function. Null modelling revealed a stronger role of stochasticity at intermediate disturbance frequencies, preceding the formation of a peak in α-diversity. Communities at extreme ends of the disturbance range had the lowest α-diversity and highest within-treatment similarity in terms of β-diversity, with stronger deterministic assembly. Stochasticity prevailed during the initial successional stages, coinciding with better specialized function (nitrogen removal). In contrast, general functions (carbon removal and microbial aggregate settleability) benefited from stronger deterministic processes. We showed that changes in assembly processes predictably precede changes in diversity under a gradient of disturbance frequencies, advancing our understanding of the mechanisms behind disturbance-diversity-function relationships.

Patterns of grassland community composition and structure along an elevational gradient on the Qinghai-Tibet Plateau

2021 ◽  
Author(s):  
Xin Wang ◽  
Jiangling Zhu ◽  
Shitao Peng ◽  
Tianli Zheng ◽  
Zhaoyu Qi ◽  
...  
Keyword(s):  
Community Composition ◽  
Elevation Gradient ◽  
Elevational Gradient ◽  
Tibet Plateau ◽  
Equation Modeling ◽  
Grassland Community ◽  
Β Diversity ◽  
Composition And Structure ◽  
Α Diversity ◽  
Qinghai Tibet Plateau

Abstract Aims Grasslands in the Qinghai-Tibet Plateau play an important role in preserving ecological security and high biodiversity in this region. However, the distribution of the composition and structure of plant community and the mechanism by which it maintains itself in this region is still poorly understood. Methods Here, we designed 195 grassland plots in 39 grassland sites along an approximately 1700-m elevation gradient on the Northeastern Qinghai-Tibet Plateau. Important findings We found that the grassland community height decreased significantly with the increase of elevation, while community coverage did not demonstrate significant changes. With the increase of elevation, the plant species richness (α diversity) increased significantly, but the community variability (β diversity) decreased significantly. The constrained clustering analysis suggested that the α- and β-diversity in the grasslands transformed gradually with elevation, and three discontinuous points (based on community structure) were observed at elevation of 3640, 4252 and 4333 m. Structural equation modeling (SEM) indicated that the increase of precipitation and the decrease of temperature significantly positively influenced α diversity, which was negatively correlated with β diversity. These results demonstrate that the community composition and structure presented a quantitative-to-qualitative change along this elevational gradient on the Qinghai-Tibet Plateau.

scholarly journals Diversity and Co-Occurrence Patterns of microbial Communities in the Fertilized Eggs of Thitarodes Insect, the Implication on the Occurrence of Chinese cordyceps

2020 ◽  
Author(s):  
Lian-Xian Guo ◽  
Xiao-Shan Liu ◽  
Zhan-Hua Mai ◽  
Yue-Hui Hong ◽  
Qi-Jiong Zhu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Network Analysis ◽  
Bacterial Community ◽  
Large Scale ◽  
Diversity Analysis ◽  
Its Sequencing ◽  
Β Diversity ◽  
Α Diversity ◽  
16S Rna ◽  
Fungal Structure

Abstract Background The large-scale artificial cultivation of Chinese cordyceps has not been widely implemented because the crucial factors triggering the occurrence of Chinese cordyceps have not been fully illuminated. Methods In this study, the bacterial and fungal structure of fertilized eggs in the host Thitarodes collected from 3 sampling sites with different occurrence rates of Chinese cordyceps (Sites A, B and C: high, low and null Chinese cordyceps, respectively) were analyzed by performing 16S RNA and ITS sequencing, respectively. And the intra-kingdom and inter-kingdom network were analyzed. Results For bacterial community, totally 4671 bacterial OTUs were obtained. α-diversity analysis revealed that the evenness of the eggs from site A was significantly higher than that of sites B and C, and the dominance index of site A was significantly lower than that of sites B and C ( P < 0.05). β-diversity analysis showed that the differences of bacterial community among the eggs from the three sampling sites were significantly different. OTU1 ( Wolbachia ) was the overwhelming predominant bacteria in the eggs from sites B and C. Although OTU4 ( Spiroplasma ) was detected in minor abundances, it showed distribution preference in the fertilized eggs from site A. For fungal community, totally 3318 fungal OTUs were obtained. Difference analysis showed significant differences among the three sites, while the differences were not as significant as that of bacterial community. In addition, ten fungal genera in the three most concerned Cordyceps families (Clavicipitaceae, Cordycipitaceae and Ophiocordycipitaceae) were detected in the fertilized eggs, while the most approved anamorph ( Hirsutella ) of Chinese cordyceps wasn’t discovered. Intra-kingdom (fungi) network analysis revealed more positive correlations and average degrees at sites A, and Inter-kingdom network analysis revealed more positive and negative correlations at sites A. Discussion The microbial community, especially the bacterial community in the fertilized eggs, might be significantly related with the occurrence of Chinese cordyceps, and Wolbachia might be the most significant microorganism negatively related with the occurrence. A closer correlation of the microbial community, especially closer fungal positive correlation, in the fertilized eggs might help for the occurrence of Chinese cordyceps.

scholarly journals The growth of plants and indigenous bacterial community were significantly affected by cadmium contamination in soil–plant system

AMB Express ◽  
2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yunyan Du ◽  
Dawei Zhang ◽  
Dinggang Zhou ◽  
Lili Liu ◽  
Jinfeng Wu ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Bacterial Community ◽  
Bacterial Communities ◽  
Anthropogenic Activities ◽  
Ecosystem Functions ◽  
Toxic Heavy Metals ◽  
Plant System ◽  
Composition And Structure ◽  
Α Diversity ◽  
The Impact

AbstractConcentrations of heavy metals continue to increase in soil environments as a result of both anthropogenic activities and natural processes. Cadmium (Cd) is one of the most toxic heavy metals and poses health risks to both humans and the ecosystem. Herein, we explore the impacts of Cd on a soil–plant system composed of oilseed rapes (Brassica napus and Brassica juncea) and bacteria. The results showed that Cd accumulation within tissues of two species of oilseed rapes enhanced with increasing concentrations of Cd in soils, and Cd treatment decreased their chlorophyll content and suppressed rapeseeds growth. Meanwhile, Cd stress induced the changes of antioxidative enzymes activities of both B. napus and B. juncea. Response to Cd of bacterial community was similar in soil-two species of oilseed rapes system. The impact of Cd on the bacterial communities of soils was greater than bacterial communities of plants (phyllosphere and endophyte). The α-diversity of bacterial community in soils declined significantly under higher Cd concentration (30 mg/kg). In addition, soil bacterial communities composition and structure were altered in the presence of higher Cd concentration. Meanwhile, the bacterial communities of bulk soils were significantly correlated with Cd, while the variation of rhizosphere soils bacterial communities were markedly correlated with Cd and other environmental factors of both soils and plants. These results suggested that Cd could affect both the growth of plants and the indigenous bacterial community in soil–plant system, which might further change ecosystem functions in soils.

scholarly journals Uncovering the relative influences of space and environment in shaping the biogeographic patterns of mangrove mollusk diversity

2019 ◽  
Vol 77 (1) ◽  
pp. 30-39
Author(s):  
Guogui Chen ◽  
Wenqing Wang ◽  
Yi Liu ◽  
Yamian Zhang ◽  
Wei Ma ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Stochastic Processes ◽  
Marine Ecology ◽  
Global Changes ◽  
Diversity Pattern ◽  
Diversity Patterns ◽  
Biogeographic Patterns ◽  
Β Diversity ◽  
Α Diversity ◽  
Deterministic Processes

Abstract Determining the relative importance of ecological processes regulating the biogeographic patterns of marine species, especially with respect to α- and β-diversity in multi-habitat communities, is a central goal in marine ecology. We explored the relative contribution of spatial (stochastic processes) and environmental factors (deterministic processes) to the biogeographic patterns of the α- and β-diversity of mangrove mollusks. A total of 16 mangrove areas were sampled in southeast coast China from 18°N to 28°N latitude. The highest mean α-diversity was found at 20°N and that of β-diversity was at 21°N. Both spatial and environmental factors had significant effects on the α- and β-diversity patterns. The environments had greater effects than the spaces on shaping the α-diversity pattern, while the spaces were relatively more important in governing the β-diversity patterns than the environments. Our results suggest that the α-diversity pattern was mainly controlled by deterministic processes (environmental filtering), while β-diversity was primarily shaped by stochastic processes (dispersal-related), although both processes had significant impacts on α- and β-diversity patterns. Identifying the ecological variables and mechanisms that drive variations in α- and β-diversity may help guide the conservation for biodiversity in endangered mangrove ecosystems under anthropogenic and global changes.

112 Modulating Effects of Miscanthus Grass and Prebiotic Blends on Canine Fecal Microbiota, Metabolites, and Digestibility

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 56-57
Author(s):  
Shannon E Finet ◽  
Fei He ◽  
Lindsay V Clark ◽  
Maria R de Godoy
Keyword(s):  
Dietary Fiber ◽  
Resistant Starch ◽  
Latin Square ◽  
Chemical Properties ◽  
Fecal Microbiota ◽  
Physiological Effects ◽  
Tomato Pomace ◽  
Β Diversity ◽  
Α Diversity ◽  
Beet Pulp

Abstract Dietary fiber plays an important role in gastrointestinal health as it modulates the gut environment and promotes microbiome homeostasis. However, dietary fiber sources vary in composition, physico-chemical properties, and physiological effects. The objective of this study was to evaluate the effects of miscanthus grass fiber and prebiotic fiber blends on fecal microbiota, fecal metabolites, and apparent total tract digestibility in comparison to traditional dietary fiber sources. Animal procedures were approved by the University of Illinois Institutional Animal Care and Use Committee. Six dietary treatments were formulated to meet or exceed AAFCO nutrient profile (2018) and included either cellulose, beet pulp, miscanthus fiber, or a blend of miscanthus fiber and tomato pomace, miscanthus fiber and resistant starch, or miscanthus fiber and fructooligosaccharide. Twelve female adult beagles were randomly assigned one of the six treatments in a replicated 6x6 Latin square design and fed for 21 d including 17 d of diet adaptation followed by 4 d of total and fresh fecal collection. All diets were well digested by the animals. Dogs fed beet pulp had greater fecal total short-chain fatty acid concentration than the cellulose treatment (P &lt; 0.05), while the dogs fed diets containing miscanthus fiber were intermediate. No difference in the α-diversity of fecal microbial communities was observed among treatments (P &gt;0.05), while β-diversity of dogs fed the beet pulp treatment differed from the other treatment groups. Miscanthus grass can be utilized successfully in diets for adult dogs with tomato pomace and resistant starch blends resulting in similar physiological effects to cellulose.

scholarly journals Contrasting Patterns in Diversity and Community Assembly of Phragmites australis Root-Associated Bacterial Communities from Different Seasons

2020 ◽  
Vol 86 (14) ◽  
Author(s):  
Rujia He ◽  
Jin Zeng ◽  
Dayong Zhao ◽  
Rui Huang ◽  
Zhongbo Yu ◽  
...  
Keyword(s):  
Phragmites Australis ◽  
Community Assembly ◽  
Bacterial Communities ◽  
Aquatic Ecosystems ◽  
Null Model ◽  
Relative Importance ◽  
Bulk Sediment ◽  
Β Diversity ◽  
Different Seasons ◽  
Deterministic Processes

ABSTRACT The common reed (Phragmites australis), a cosmopolitan aquatic macrophyte, plays an important role in the structure and function of aquatic ecosystems. We compared bacterial community compositions (BCCs) and their assembly processes in the root-associated compartments (i.e., rhizosphere and endosphere) of reed and bulk sediment between summer and winter. The BCCs were analyzed using high-throughput sequencing of the bacterial 16S rRNA gene; meanwhile, null-model analysis was employed to characterize their assembly mechanisms. The sources of the endosphere BCCs were quantitatively examined using SourceTracker from bulk sediment, rhizosphere, and seed. We observed the highest α-diversity and the lowest β-diversity of BCCs in the rhizosphere in both seasons. We also found a significant increase in α- and β-diversity in summer compared to that in winter among the three compartments. It was demonstrated that rhizosphere sediments were the main source (∼70%) of root endosphere bacteria during both seasons. Null-model tests indicated that stochastic processes primarily affected endosphere BCCs, whereas both deterministic and stochastic processes dictated bacterial assemblages of the rhizosphere, with the relative importance of stochastic versus deterministic processes depending on the season. This study suggests that multiple mechanisms of bacterial selection and community assembly exist both inside and outside P. australis roots in different seasons. IMPORTANCE Understanding the composition and assembly mechanisms of root-associated microbial communities of plants is crucial for understanding the interactions between plants and soil. Most previous studies of the plant root-associated microbiome focused on model and economic plants, with fewer temporal or seasonal investigations. The assembly mechanisms of root-associated bacterial communities in different seasons remain poorly known, especially for the aquatic macrophytes. In this study, we compared the diversity, composition, and relative importance of two different assembly processes (stochastic and deterministic processes) of bacterial communities associated with bulk sediment and the rhizosphere and endosphere of Phragmites australis in summer and winter. While we found apparent differences in composition, diversity, and assembly processes of bacterial communities among different compartments, season played important roles in determining BCCs and their diversity patterns and assemblages. We also found that endosphere bacteria mainly originated from the rhizosphere. The results add new knowledge regarding the plant-microbe interactions in aquatic ecosystems.

Sign in / Sign up

Export Citation Format

Share Document