ABSTRACT
A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. ...After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is still complicated and time-consuming. To address this problem, we present an integrated R package-‘microeco’ as an analysis pipeline for treating microbial community and environmental data. This package was developed based on the R6 class system and combines a series of commonly used and advanced approaches in microbial community ecology research. The package includes classes for data preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta diversity analysis, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis. Each class is designed to provide a set of approaches that can be easily accessible to users. Compared with other R packages in the microbial ecology field, the microeco package is fast, flexible and modularized to use and provides powerful and convenient tools for researchers. The microeco package can be installed from CRAN (The Comprehensive R Archive Network) or github (https://github.com/ChiLiubio/microeco).
An integrated and powerful R package-microeco was developed for researchers to perform data mining of amplicon sequencing in microbial community ecology.
Rhizosphere bacteria have significant contributions to crop health, productivity and carbon sequestration. As maize (Zea mays) is an important economic crop, its rhizosphere bacterial communities ...have been intensively investigated using various approaches. However, low-resolution profiling methods often make it difficult to understand the complicated rhizosphere bacterial communities and their dynamics. In this study, we analyzed growth-stage related dynamics of bacterial community structures in the rhizosphere of maize using the pyrosequencing method, which revealed an assembly of bacteria enriched in the rhizosphere. Our results revealed that the rhizosphere of maize was preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum was represented by one or two dominating subsets of bacterial groups. Dominant genera enriched in the rhizosphere included Massilia, Burkholderia, Ralstonia, Dyella, Chitinophaga and Sphingobium. Rhizosphere bacterial community structures significantly changed through different growth stages at lower taxonomic ranks (family, genus and OTU levels). Genera Massilia, Flavobacterium, Arenimonas and Ohtaekwangia were relatively abundant at early growth stages, while genera Burkholderia, Ralstonia, Dyella, Chitinophaga, Sphingobium, Bradyrhizobium and Variovorax populations were dominant at later stages. Comparisons of pyrosequencing data collected in Illinois, USA in this study with the available data from Braunschweig, Germany indicated many common bacterial inhabitants but also many differences in the structure of bacterial communities, implying that some site-specific factors, such as soil properties, may play important roles in shaping the structure of rhizosphere bacterial community.
•Maize rhizosphere bacterial community was surveyed using 16S rRNA pyrosequencing.•Early and late plant growth stages had distinctive rhizosphere communities.•Members of Burkholderiales showed the most dynamic changes with root growth stage.•Location-specific differences in maize rhizosphere occur below the genus level.
Seasonal dynamics of soil microbial communities may influence ecosystem functions and services. However, few observations have been conducted on the dynamics of a bacterial community assembly across ...seasons in different elevations in mountain forest ecosystems. In this study, the diversity, compositions, community assembly processes, and co-occurrence interactions of soil bacterial communities were investigated using Illumina sequencing of 16S rRNA genes across different seasons during two consecutive years (2016 and 2017) at two elevational sites in Mount Gongga, China. These two sites included an evergreen broad-leaved forest (EBF, 2100 m a.s.l.) and a dark coniferous forest (DCF, 3000 m a.s.l.). The results showed that bacterial diversity and structure varied considerably between the two elevational sites with only limited seasonal variations. Interannuality had a significant effect on the diversity and structure of soil bacterial communities. The bacterial alpha diversity was significantly higher at site EBF(e.g., OTUs richness, 2207 ± 276) than at site DCF(e.g., OTUs richness, 1826 ± 315). Soil pH, temperature, elevation, and water content were identified as important factors shaping soil bacterial communities in the mountain forests. Bacterial community assembly was primarily governed by deterministic processes regardless of elevation and season. Deterministic processes were stronger at site DCF than at EBF. The soil bacterial community at site EBF harbored a more complex and connected network with less resistance to environmental changes. Overall, this study showed that seasonal dynamics of bacterial communities were much weaker than those along elevations, implying that a single-season survey on a bacterial community along an elevational gradient can represent overall changes in the bacterial community.
Key points
• Seasonal dynamics of soil bacterial communities were studied in Mount Gongga.
• The bacterial community was mainly affected by elevation rather than season.
• Deterministic processes dominated bacterial community assembly.
• The bacterial network was more complex but less stable at EBF than at DCF.
Abstract
Biodiversity patterns across geographical gradients could result from regional species pool and local community assembly mechanisms. However, little has been done to separate the effects of ...local ecological mechanisms from variation in the regional species pools on bacterial diversity patterns. In this study, we compare assembly mechanisms of soil bacterial communities in 660 plots from 11 regions along a latitudinal gradient in eastern China with highly divergent species pools. Our results show that β diversity does not co-vary with γ diversity, and local community assembly mechanisms appear to explain variation in β diversity patterns after correcting for variation in regional species pools. The variation in environmental conditions along the latitudinal gradient accounts for the variation in β diversity through mediating the strength of heterogeneous selection. In conclusion, our study clearly illustrates the importance of local community assembly processes in shaping geographical patterns of soil bacterial β diversity.
Interspecies electron transfer is common in methanogenic consortia. Syntrophic partners cooperate by transferring electrons from one species to the other using H2, formate or other pathways, and ...maintaining H2 at low levels, so that the overall reactions are thermodynamically more favorable. Here we reviewed the mechanisms of interspecies electron transfer involved in methanogenic consortia, i.e., interspecies H2 transfer, interspecies formate transfer, and direct interspecies electron transfer (DIET) via pili, and/or outer membrane cytochromes. Although the relative importance of different mechanisms is uncertain, one mechanism may predominate under specific circumstances. Interspecies electron transfer is a probable mechanism in anaerobic granules formed in upflow anaerobic sludge bed (UASB) reactors, though direct evidence is limited. Studies of interspecies electron transfer without extracellular shuttles are mainly confined to Shewanella and Geobacter species. These mechanisms could be more energy-conserving than interspecies H2 or formate transfer, but the relationship between them is yet unelucidated. These studies are meaningful in that they could enable us a deeper understanding of how microorganisms degrade waste and produce biogas, and how current waste treatment and methane production strategies could be improved.
Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, ...microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4(+), lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.
Ecological understandings of soil bacterial community succession and assembly mechanism along elevational gradients in mountains remain not well understood. Here, by employing the high-throughput ...sequencing technique, we systematically examined soil bacterial diversity patterns, the driving factors, and community assembly mechanisms along the elevational gradients of 1800-4100 m on Gongga Mountain in China. Soil bacterial diversity showed an extraordinary stair-step pattern along the elevational gradients. There was an abrupt decrease of bacterial diversity between 2600 and 2800 m, while no significant change at either lower (1800-2600 m) or higher (2800-4100 m) elevations, which coincided with the variation in soil pH. In addition, the community structure differed significantly between the lower and higher elevations, which could be primarily attributed to shifts in soil pH and vegetation types. Although there was no direct effect of MAP and MAT on bacterial community structure, our partial least squares path modeling analysis indicated that bacterial communities were indirectly influenced by climate via the effect on vegetation and the derived effect on soil properties. As for bacterial community assembly mechanisms, the null model analysis suggested that environmental filtering played an overwhelming role in the assembly of bacterial communities in this region. In addition, variation partition analysis indicated that, at lower elevations, environmental attributes explained much larger fraction of the β-deviation than spatial attributes, while spatial attributes increased their contributions at higher elevations. Our results highlight the importance of environmental filtering, as well as elevation-related spatial attributes in structuring soil bacterial communities in mountain ecosystems.
•Temperature-regulated mechanism in AD process is revealed by metatranscriptome.•Methanogenesis and oxidative phosphorylation are enhanced at elevated temperature.•Function centralization is crucial ...for the efficiency of AD system function.•Temperature regulates AD process by the centralization of functional pathways.
Temperature is crucial for the performance of anaerobic digestion process. In this study of anaerobic digestion of swine manure, the relationship between the microbial gene expression and methane production at different temperatures (25–55°C) was revealed through metatranscriptomic analysis. Daily methane production and total biogas production increased with temperature up to 50°C, but decreased at 55°C. The functional gene expression showed great variation at different temperatures. The function centralization (opposite to alpha-diversity), assessed by the least proportions of functional pathways contributing for at least 50% of total reads positively correlated to methane production. Temperature regulated methane production probably through reducing the diversity of functional pathways, but enhancing central functional pathways, so that most of cellular activities and resource were invested in methanogenesis and related pathways, enhancing the efficiency of conversion of substrates to methane. This research demonstrated the importance of function centralization for efficient system functioning.
The soil microbial community plays an important role in terrestrial carbon and nitrogen cycling. However, microbial responses to climate warming or cooling remain poorly understood, limiting our ...ability to predict the consequences of future climate changes. To address this issue, it is critical to identify microbes sensitive to climate change and key driving factors shifting microbial communities. In this study, alpine soil transplant experiments were conducted downward or upward along an elevation gradient between 3,200 and 3,800 m in the Qinghai-Tibet plateau to simulate climate warming or cooling. After a 2-year soil transplant experiment, soil bacterial communities were analyzed by pyrosequencing of 16S rRNA gene amplicons. The results showed that the transplanted soil bacterial communities became more similar to those in their destination sites and more different from those in their "home" sites. Warming led to increases in the relative abundances in Alphaproteobacteria, Gammaproteobacteria, and Actinobacteria and decreases in Acidobacteria, Betaproteobacteria, and Deltaproteobacteria, while cooling had opposite effects on bacterial communities (symmetric response). Soil temperature and plant biomass contributed significantly to shaping the bacterial community structure. Overall, climate warming or cooling shifted the soil bacterial community structure mainly through species sorting, and such a shift might correlate to important biogeochemical processes such as greenhouse gas emissions. This study provides new insights into our understanding of soil bacterial community responses to climate warming and cooling.
Soil diazotrophs possess the function of fixing atmospheric N2 into biologically available ammonium in terrestrial ecosystems. However, there are limited studies into how diazotrophic communities ...change when grassland environments differ. In this study, we elucidated the diversity and interactions of diazotrophic communities in three steppe types of Inner Mongolia, China, including non-desert steppe (MT), desert steppe (D) and sandy steppe (S). We expected to improve the predictions of diazotrophic responses to grassland degradation at time gradients based on their discrepancies among steppe types along spatial gradients. Steppe types affected the alpha- and beta-diversity of diazotrophic communities, which were mainly controlled by plant biomass and soil pH, respectively. Diazotrophic communities were strongly aggregated with their respective steppe environments, but dissimilar under different types according to Bray-Curtis distance. In addition, network analysis showed that the network structure of diazotrophs from the D was relatively simpler than the other two types (MT and S). More exclusionary relationships in diazotrophic communities occurred in the D and S steppes than in the MT steppe. The species shared across the steppes changed their interactions with other species to adapt to different habitats. Moreover, different steppes had distinct key species to underpin the whole network. The disturbances or extinctions of these key species may lead to the instability of the diazotrophic co-occurrence network. Overall, we speculate that if grassland degradation happens, the change of grassland microenvironment may mediate the differences in the diversity and co-occurrence patterns of diazotrophs, allowing them to adapt to environmental changes.
•Steppe types shape the alpha and beta-diversity of diazotrophs.•Steppe types impact the interactions of diazotrophs..•Steppe degradation may change the diversity and co-occurrence patterns of diazotrophs.
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