scholarly journals Bridging Rare and Abundant Bacteria with Ecosystem Multifunctionality in Salinized Agricultural Soils: from Community Diversity to Environmental Adaptation

mSystems ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Wenjie Wan ◽  
Song Liu ◽  
Xiang Li ◽  
Yonghui Xing ◽  
Wenli Chen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Variable Selection ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Agricultural Soils ◽  
Environmental Adaptation ◽  
Community Diversity ◽  
Soil Restoration ◽  
Α Diversity ◽  
Ecosystem Multifunctionality

ABSTRACT Bacterial diversity and ecosystem multifunctionality (EMF) vary along environmental gradients. However, little is known about interconnections between EMF and taxonomic and phylogenetic diversities of rare and abundant bacteria. Using MiSeq sequencing and multiple statistical analyses, we evaluated the maintenance of taxonomic and phylogenetic diversities of rare and abundant bacteria and their contributions to EMF in salinized agricultural soils (0.09 to 19.91 dS/m). Rare bacteria exhibited closer phylogenetic clustering and broader environmental breadths than abundant ones, while abundant bacteria showed higher functional redundancies and stronger phylogenetic signals of ecological preferences than rare ones. Variable selection (86.7%) dominated rare bacterial community assembly, and dispersal limitation (54.7%) and variable selection (24.5%) determined abundant bacterial community assembly. Salinity played a decisive role in mediating the balance between stochastic and deterministic processes and showed significant effects on functions and diversities of both rare and abundant bacteria. Rare bacterial taxonomic α-diversity and abundant bacterial phylogenetic α-diversity contributed significantly to EMF, while abundant bacterial taxonomic α-diversity and rare bacterial phylogenetic α-diversity did not. Additionally, abundant rather than rare bacterial community function had a significant effect on soil EMF. These findings extend our knowledge of environmental adaptation of rare and abundant bacteria and highlight different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF. IMPORTANCE Soil salinization is a worldwide environmental problem and threatens plant productivity and microbial diversity. Understanding the generation and maintenance of microbial diversity is essential to estimate soil tillage potential via investigating ecosystem multifunctionality. Our sequence-based data showed differences in environmental adaptations of rare and abundant bacteria at taxonomic and phylogenetic levels, which led to different contributions of taxonomic and phylogenetic α-diversities of rare and abundant bacteria to soil EMF. Studying the diversity of rare and abundant bacteria and their contributions to EMF in salinized soils is critical for guiding soil restoration.

scholarly journals Phyllosphere community assembly and response to drought stress on common tropical and temperate forage grasses

2021 ◽  
Author(s):  
Emily K. Bechtold ◽  
Stephanie Ryan ◽  
Sarah E. Moughan ◽  
Ravi Ranjan ◽  
Klaus Nüsslein
Keyword(s):  
Microbial Community ◽  
Drought Stress ◽  
Bacterial Community ◽  
Community Assembly ◽  
Community Diversity ◽  
Grass Species ◽  
Severe Drought ◽  
Hormone Production ◽  
Plant Host ◽  
Bacterial Community Diversity

Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future.

scholarly journals Deciphering Centimeter-Scale Microbial Biogeographic Patterns and Community Assembly Processes From A 3D Perspective

2020 ◽  
Author(s):  
Ran Xue ◽  
Kankan Zhao ◽  
Xiuling Yu ◽  
Erinne Stirling ◽  
Shan Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Variable Selection ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Sampling Strategy ◽  
Sampling Scheme ◽  
Ecological Processes ◽  
Soil Matrix ◽  
Biogeographic Patterns ◽  
2D To 3D

Abstract Background: Revealing the effects of multi-dimensional spatial distribution on microorganisms is crucial for the further understanding of microbial diversity, turnover and ecological processes. However, microbial community assembly and the factors that shape it are still unknown from a three dimensional (3D) perspective. Here, a 3D model was created by performing an exhaustive sampling strategy to a 4x4x4 soil matrix. We examined the dynamics of microbial diversity, biogeographic patterns and microbial assembly processes when transfroming sampling scheme from 2D to 3D.Results: Our results indicated that dispersion of microbial community and significance of distance decay relationship was higher in the 3D compared with 2D sampling scheme, suggesting increased microbial turnover when transforming the model from 2D to 3D. Only a small fraction of community variation can be explained by environmental, spatial factors and spatial canonical axes, possibly due to unmeasured environmental variables. The assembly of microbial community was dominated by deterministic processes that shifted from homogeneous selection to variable selection as we transformed the model from 2D to 3D. The importance of stochasticity increased when homogeneous and variable selection processes were well balanced. However, heterogeneity of existing environmental and spatial variables failed to explain the dynamics of community assembly.Conclusions: Our study revealed significant dynamics of microbial diversity and assembly processes when assessed from 2D and 3D perspectives. As microorganisms are spatially distributed in soil, this spatial dependent diversity and assembly suggests that microbial ecological questions need to be considered in more dimensions than they usually are. Further, new models that integrate all data sets are still needed to disengle the microbial processes in multiple dimensions.

scholarly journals Assembly Processes and Co-occurrence Patterns of Abundant and Rare Bacterial Community in the Eastern Indian Ocean

2021 ◽  
Vol 12 ◽  
Author(s):  
Liuyang Li ◽  
Laxman Pujari ◽  
Chao Wu ◽  
Danyue Huang ◽  
Yuqiu Wei ◽  
...  
Keyword(s):  
Microbial Community ◽  
Indian Ocean ◽  
Bacterial Community ◽  
Variable Selection ◽  
Rare Species ◽  
Abundant Species ◽  
Community Diversity ◽  
Eastern Indian Ocean ◽  
Rare Taxa ◽  
Deterministic Processes

Microbial communities are composed of many rare species and a few abundant species. Considering the disproportionate importance of rare species for ecosystem functioning, it is important to understand the mechanisms structuring the rare and abundant components of a diverse community in response to environmental changes. Here, we used a 16S ribosomal RNA gene sequencing approach to investigate the bacterial community diversity in the Eastern Indian Ocean (EIO) during the monsoon and intermonsoon. We employed a phylogenetic null model and network analysis to evaluate the assembly processes and co-occurrence pattern of the microbial community. We found that higher bacterial diversity was detected in the intermonsoon with high temperature and low Chlorophyll a concentrations and N/P ratios. The balance between ecological deterministic processes and stochastic processes varied with seasons in the EIO. Meanwhile, conditionally rare taxa (CRT) were more likely modulated by variable selection processes than always rare taxa (ART) and abundant taxa (AT) (CRT > ART > AT). By linking assembly process and species co-occurrence, we demonstrated that the microbial co-occurrence associations tended to be higher when deterministic processes (mainly variable selection) were weaker. This negative trend was observed in rare species rather than abundant species. The linkage could enhance our understanding of the underlying mechanisms underpinning the generation and maintenance of microbial community diversity.

scholarly journals Gut microbiome features associated withClostridium difficilecolonization in puppies

2019 ◽  
Author(s):  
Alexander S. Berry ◽  
Denise Barnhart ◽  
Brendan J. Kelly ◽  
Donna J. Kelly ◽  
Daniel P. Beiting ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Gut Microbiome ◽  
Statistical Significance ◽  
Random Effect ◽  
Mixed Effects ◽  
Community Diversity ◽  
Bacterial Community Diversity ◽  
Gut Microbial Community ◽  
Colonization Status

AbstractIn people, colonization withClostridium difficile, the leading cause of antibiotic-associated diarrhea, has been shown to be associated with distinct gut microbial features, including reduced bacterial community diversity and depletion of key taxa. In dogs, the gut microbiome features that defineC. difficilecolonization are less well understood. We sought to define the gut microbiome features associated withC. difficilecolonization in puppies, a population where the prevalence ofC. difficilehas been shown to be elevated, and to define the effect of puppy age and litter upon these features andC. difficilerisk. We collected fecal samples from weaned (n=27) and unweaned (n=74) puppies from 13 litters and analyzed the effects of colonization status, age and litter on microbial diversity using linear mixed effects models.Colonization withC. difficilewas significantly associated with younger age, and colonized puppies had significantly decreased bacterial community diversity and differentially abundant taxa compared to non-colonized puppies, even when adjusting for age.C. difficilecolonization remained associated with decreased bacterial community diversity, but the association did not reach statistical significance in a mixed effects model incorporating litter as a random effect.Even though litter explained a greater proportion (67%) of the variability in microbial diversity than colonization status, we nevertheless observed heterogeneity in gut microbial community diversity and colonization status within more than half of the litters, suggesting that the gut microbiome contributes to colonization resistance againstC. difficile. The colonization of puppies withC. difficilehas important implications for the potential zoonotic transfer of this organism to people. The identified associations point to mechanisms by whichC. difficilecolonization may be reduced.

scholarly journals Fungal alpha-diversity drives the stochasticity of bacterial and fungal community assembly in soil aggregates in the apple orchard

2020 ◽  
Author(s):  
Wei Zheng ◽  
Zhiyuan Zhao ◽  
Fenglian Lv ◽  
Yanan Yin ◽  
Zhaohui Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Fungal Community ◽  
Community Assembly ◽  
Fungal Diversity ◽  
Soil Aggregates ◽  
Alpha Diversity ◽  
Apple Orchard ◽  
Community Diversity ◽  
Agricultural Practice ◽  
Bacteria And Fungi

Abstract Background In soil ecosystems, bacteria and fungi always co-exist in the same niche and interact with each other, especially in different sized soil aggregates. The bacterial and fungal community assembly process and bacteria-fungi interactions in soil aggregates, which is important for bacterial and fungal community diversity and composition, is still unclear.Methods We examined bacterial and fungal community assembly in soil macroaggregate (> 0.25 mm), microaggregate (0.053–0.25 mm) and smaller microaggregate (silt + clay, < 0.053 mm) in an apple orchard. The microbial community assembly processes were analyzed by normalized stochasticity ratio index (NST).Results Bacterial community diversity, composition and assembly were more affected by agricultural practice and aggregate than fungal community. Bacterial community assembly was more stochastic in silt + clay than in macroaggregate, and was more stochastic (NST > 50%) than fungal community in soil aggregates. Meanwhile, bacterial NST was negatively correlated with fungal diversity, and fungal NST was positively correlated with fungal diversity. Co-occurrence network suggested that the bacteria and fungi were less strongly interacting in the network of silt + clay, compared to macroaggregate. The results indicated that fungi impact on the bacterial community assembly in soil aggregate, and the stochasticity of bacterial community assembly was increased with the decrease of interaction between bacteria and fungi in soil aggregates.Conclusions This study enhances our understanding of the mechanism of bacterial and fungal community assembly and co-exists pattern of bacteria and fungi in soil aggregates.

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.

High Salinity Inhibits Soil Bacterial Community Mediating Nitrogen Cycling

2021 ◽  
Author(s):  
Xiang Li ◽  
Achen Wang ◽  
Wenjie Wan ◽  
Xuesong Luo ◽  
Liuxia Zheng ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Variable Selection ◽  
Nitrogen Cycling ◽  
Community Composition ◽  
Community Assembly ◽  
High Salinity ◽  
Bacterial Community Composition ◽  
Soil Bacterial Community ◽  
Saline Soils ◽  
Soil Bacterial

Salinization is considered as a major threat to soil fertility and agricultural productivity throughout the world. Soil microbes play a crucial role in maintaining ecosystem stability and function (e.g., nitrogen cycling). However, the response of bacterial community composition and community-level function to soil salinity remains uncertain. Herein, we used multiple statistical analyses to assess the effect of high salinity on bacterial community composition and potential metabolism function in the agricultural ecosystem. Results showed that high salinity significantly altered bacterial both alpha (Shannon-Wiener index and phylogenetic diversity) and beta diversity. Salinity, TN, and SOM were the vital environmental factors shaping bacterial community composition. The relative abundance of Actinobacteria , Chloroflexi , Acidobacteria , and Planctomycetes decreased with salinity, whereas Proteobacteria and Bacteroidetes increased with salinity. The modularity and the ratio of negative to positive links remarkedly decreased indicated that high salinity destabilized bacterial networks. Variable selection, which belongs to deterministic processes, mediated bacterial community assembly within the saline soils. Function prediction results showed that the key nitrogen metabolism (e.g., ammonification, nitrogen fixation, nitrification, and denitrification processes) was inhibited in high salinity habitats. Miseq sequencing of 16S rRNA genes revealed that the abundance and composition of nitrifying community were influenced by high salinity. The consistency of function prediction and experimental verification demonstrated that high salinity inhibited soil bacterial community mediating nitrogen cycling. Our study provides strong evidence for salinity effect on the bacterial community composition and key metabolism function, which could help us understand how soil microbe responds to ongoing environment perturbation. IMPORTANCE Revealing the response of the soil bacterial community to external environmental disturbances is an important but poorly understood topic in microbial ecology. In this study, we evaluated the effect of high salinity on the bacterial community composition and key biogeochemical processes in salinized agricultural soils (0.22 to 19.98 dS m −1 ). Our results showed that high salinity significantly decreased bacterial diversity, altered bacterial community composition, and destabilized bacterial network. Moreover, variable selection (61-66%) mediated bacterial community assembly within the saline soils. Functional prediction combined with microbiological verification proved that high salinity inhibited soil bacterial community mediating nitrogen turnover. Understanding the impact of salinity on soil bacterial community is of great significance in managing saline soils and maintaining a healthy ecosystem.

scholarly journals Phyllosphere Community Assembly and Response to Drought Stresson Common Tropical and Temperate Forage Grasses

2021 ◽  
Author(s):  
Emily K. Bechtold ◽  
Stephanie Ryan ◽  
Sarah E. Moughan ◽  
Ravi Ranjan ◽  
Klaus Nüsslein
Keyword(s):  
Microbial Community ◽  
Drought Stress ◽  
Bacterial Community ◽  
Community Assembly ◽  
Community Diversity ◽  
Grass Species ◽  
Plant Host ◽  
Bacterial Community Diversity ◽  
Climate Stress ◽  
Drought Conditions

Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future. IMPORTANCE Globally important grassland ecosystems are at risk of degradation due to poor management practices compounded by predicted increases in severity and duration of drought over the next century. Finding new ways to support grassland productivity is critical to maintaining their ecological and agricultural benefits. Discerning how grassland microbial communities change in response to climate stress will help us understand how plant-microbe relationships may be useful to sustainably support grasslands in the future. In this study, phyllosphere community diversity and composition was significantly altered under drought conditions. The significance of our research is demonstrating how severe climate stress reduces bacterial community diversity, which previously was directly associated with decreased plant productivity. These findings guide future questions about functional plant-microbe interactions under stress conditions, greatly enhancing our understanding of how bacteria can increase food security by promoting grassland growth and resilience.

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