Maize (Zea Mays L.) Genotypes Induce the Changes of Rhizosphere Microbial Communities

Abstract Plant-microbe interactions affect ecosystem function, and plant species influence relevant microorganisms. However, the different genotypes of maize that shape the structure and function of the rhizosphere microbial community remain poorly investigated. During this study, the structures of the rhizosphere microbial community among three genotypes of maize were analyzed at the seedling and maturity stages using high-throughput sequencing and bioinformatics analysis. The results demonstrated that Tiannuozao 60 (N) showed higher bacterial and fungal diversity in both periods, while Junlong1217 (QZ) and Fujitai519 (ZL) had lower diversity. The bacterial community structure among the three varieties was significantly different; however, fewer differences were found in the fungal community. The bacterial community composition of N and QZ was similar yet different from ZL at the seedling stage. The bacterial networks of the three cultivars were more complex than the fungal networks, and the networks of the mature stages were more complex than those of the seedling stages, while the opposite was true for the fungi. FAPROTAX functional and FUNGuild functional predictions revealed that different varieties of maize were different in functional abundance at the genus level, and these differences were related to breeding characteristics. This study suggested that different maize genotypes regulated the rhizosphere bacterial and fungal communities, which would help guide practices.

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Uncovering the Structure and Function of Microbial Communities Formed During Periodic Tilling of TNT and DNT Co-Contaminated Soils

10.1101/2020.12.12.420737 ◽

2020 ◽

Author(s):

Saeed Keshani Langroodi ◽

Yemin Lan ◽

Ben Stenuit ◽

Gail Rosen ◽

Joseph B Hughes ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Contaminated Soils ◽

Bacterial Community Composition ◽

Amplicon Sequencing ◽

Metagenomic Data ◽

Military Conflict ◽

Nitro Explosives ◽

And Function ◽

Aerobic And Anaerobic

Environmental contamination by 2,4,6-trinitrotoluene (TNT), historically the most widely used secondary explosive, is a long-standing problem in former military conflict areas and at manufacturing and decommissioning plants. In field test plots at a former explosives manufacturing site, removal of TNT and dinitrotoluenes (DNTs) was observed following periods of tillage. Since tilling of soils has previously been shown to alter the microbial community, this study was aimed at understanding how the microbial community is altered in soils with historical contamination of nitro explosives from the former Barksdale TNT plant. Samples of untilled pristine soils, untilled TNT-contaminated soils and tilled TNT-contaminated soils were subjected to targeted amplicon sequencing of 16S ribosomal RNA genes in order to compare the structure of their bacterial communities. In addition, metagenomic data generated from the TNT tilled soil was used to understand the potential functions of the bacterial community relevant to nitroaromatic degradation. While the biodiversity dropped and the Burkholderiales order became dominant in both tilled and untilled soil regardless of tillage, the bacterial community composition at finer taxonomic levels revealed a greater difference between the two treatments. Functional analysis of metagenome assembled genome (MAG) bins through systematic review of commonly proposed DNT and TNT biotransformation pathways suggested that both aerobic and anaerobic degradation pathways were present. A proposed pathway that considers both aerobic and anaerobic steps in the degradation of TNT in the scenario of the tilled contaminated soils is presented.

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Deciphering the Shifts in Microbial Community Diversity From Material Pretreatment to Saccharification Process of Fuyu-Flavor Baijiu

Frontiers in Microbiology ◽

10.3389/fmicb.2021.705967 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jiamu Kang ◽

Yunan Hu ◽

Ziyuan Ding ◽

Li Ye ◽

Haoran Li ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Fungal Community ◽

High Throughput Sequencing ◽

Raw Materials ◽

Bacterial Community Composition ◽

Community Diversity ◽

Raw Material ◽

Microbial Community Diversity ◽

Fungal Community Structure

The microbiota of the pretreatment phase is crucial to the assembly of the microbial community in the saccharification of fuyu-flavor baijiu. This study investigates the shifts in microbial community diversity from the pretreatment of raw materials to the end of saccharification. High-throughput sequencing reveals that Lactobacillus, Weissella, and Bacillus in the bacterial community and Rhizopus, Candida, Pichia, and Aspergillus in the fungal community are predominant during raw material pretreatment and saccharification processes. Also, 11 bacterial genera, including Bacillus, Lactobacillus, Leuconostoc, Weissella, Lactococcus, and Acetobacter, and eight yeast genera, including Candida, Pichia, Saccharomyces, and Wickerhamomyces, were isolated from the initial saccharification stage by culture-dependent approaches. Sourcetracker analysis indicates that the cooling grains and rice husks were the main contributors to the bacterial community composition of the saccharification process, and Qu was the main contributor to the shaping of the fungal community structure during the saccharification process. Abundance variation of the predictive functional profiles of microbial communities encoding for key enzymes involved in pyruvate metabolism, starch and sucrose metabolism, and glycolysis/gluconeogenesis during the pretreatment and saccharification phases were inferred by PICRUSt2 analysis. The results of this study will be utilized to produce consistently high-quality fuyu-flavor baijiu via better controlling the shaping of microbial community structures during the pretreatment and fermentation processes.

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Plant phenology influences rhizosphere microbial community and is accelerated by serpentine microorganisms in Plantago erecta

10.1101/2021.03.29.437500 ◽

2021 ◽

Author(s):

Alexandria N. Igwe ◽

Bibi Quasem ◽

Naomi Liu ◽

Rachel L. Vannette

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Plant Development ◽

Soil Chemistry ◽

Bacterial Species ◽

Bacterial Community Composition ◽

Serpentine Soils ◽

Microbe Interactions ◽

And Function ◽

Over Time

ABSTRACTSerpentine soils are drought-prone and rich in heavy metals, and plants growing on serpentine soils host distinct microbial communities that may affect plant survival and phenotype. However, whether the rhizosphere communities of plants from different soil chemistries are initially distinct or diverge over time may help us understand drivers of microbial community structure and function in stressful soils. Here, we test the hypothesis that rhizosphere microbial communities will converge over time (plant development), independent of soil chemistry and microbial source. We grew Plantago erecta in serpentine or nonserpentine soil, with serpentine or nonserpentine microbes and tracked plant growth and root phenotypes. We used 16S rRNA barcoding to compare bacterial species composition at seedling, vegetative, early-, and late-flowering phases. Plant phenotype and rhizosphere bacterial communities were mainly structured by soil type, with minor contributions by plant development, microbe source and their interactions. Serpentine microorganisms promoted early flowering in plants on non-serpentine soils. Despite strong effects of soil chemistry, the convergence in bacterial community composition across development demonstrates the importance of the plant-microbe interactions in shaping microbial assembly processes across soil types.

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Soil Bacterial Community Diversity and Composition as Affected by Tillage Intensity Treatments in Corn-Soybean Production Systems

Microbiology Research ◽

10.3390/microbiolres12010012 ◽

2021 ◽

Vol 12 (1) ◽

pp. 157-172

Author(s):

Shankar G. Shanmugam ◽

Normie W. Buehring ◽

Jon D. Prevost ◽

William L. Kingery

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Production System ◽

Soil Microbial Community ◽

Production Systems ◽

Bacterial Community Composition ◽

Soybean Production ◽

Soil Microbial ◽

Soil Bacterial

Our understanding on the effects of tillage intensity on the soil microbial community structure and composition in crop production systems are limited. This study evaluated the soil microbial community composition and diversity under different tillage management systems in an effort to identify management practices that effectively support sustainable agriculture. We report results from a three-year study to determine the effects on changes in soil microbial diversity and composition from four tillage intensity treatments and two residue management treatments in a corn-soybean production system using Illumina high-throughput sequencing of 16S rRNA genes. Soil samples were collected from tillage treatments at locations in the Southern Coastal Plain (Verona, Mississippi, USA) and Southern Mississippi River Alluvium (Stoneville, Mississippi, USA) for soil analysis and bacterial community characterization. Our results indicated that different tillage intensity treatments differentially changed the relative abundances of bacterial phyla. The Mantel test of correlations indicated that differences among bacterial community composition were significantly influenced by tillage regime (rM = 0.39, p ≤ 0.0001). Simpson’s reciprocal diversity index indicated greater bacterial diversity with reduction in tillage intensity for each year and study location. For both study sites, differences in tillage intensity had significant influence on the abundance of Proteobacteria. The shift in the soil bacterial community composition under different tillage systems was strongly correlated to changes in labile carbon pool in the system and how it affected the microbial metabolism. This study indicates that soil management through tillage intensity regime had a profound influence on diversity and composition of soil bacterial communities in a corn-soybean production system.

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Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions

Frontiers in Microbiology ◽

10.3389/fmicb.2021.652031 ◽

2021 ◽

Vol 12 ◽

Author(s):

Matteo Daghio ◽

Francesca Ciucci ◽

Arianna Buccioni ◽

Alice Cappucci ◽

Laura Casarosa ◽

...

Keyword(s):

Bacterial Community ◽

Growth Performance ◽

Community Composition ◽

Lipid Composition ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Daily Weight Gain ◽

Rrna Gene ◽

Rumen Microbiota ◽

Cattle Breeds

The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.

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Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome

mSystems ◽

10.1128/msystems.00511-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 5

Author(s):

Holly L. Lutz ◽

Elliot W. Jackson ◽

Paul W. Webala ◽

Waswa S. Babyesiza ◽

Julian C. Kerbis Peterhans ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Evolutionary History ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Anatomical Site ◽

Skin Microbiota ◽

Host Identity ◽

Host Ecology

ABSTRACT Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals. IMPORTANCE This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.

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Miscanthus cultivation shapes rhizosphere microbial community structure and function as assessed by Illumina MiSeq sequencing combined with PICRUSt and FUNGUIld analyses

Archives of Microbiology ◽

10.1007/s00203-020-01830-1 ◽

2020 ◽

Vol 202 (5) ◽

pp. 1157-1171

Author(s):

Yan Chen ◽

Wei Tian ◽

Yang Shao ◽

Ying-Jun Li ◽

Li-An Lin ◽

...

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Illumina Miseq ◽

Structure And Function ◽

Illumina Miseq Sequencing ◽

Miseq Sequencing ◽

And Function ◽

Rhizosphere Microbial Community

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Bacterial Community Analysis of Mine Contaminated Soils in Hechi City

Journal of Biobased Materials and Bioenergy ◽

10.1166/jbmb.2020.1967 ◽

2020 ◽

Vol 14 (4) ◽

pp. 476-486

Author(s):

Tingting Liu ◽

Caoping Pang ◽

Fengcai Ye ◽

Dafei Gong ◽

Jieling Luo ◽

...

Keyword(s):

Microbial Community ◽

Genetic Engineering ◽

Bacterial Community ◽

Contaminated Soils ◽

High Throughput Sequencing ◽

Community Analysis ◽

Microbial Community Analysis ◽

Mine Soils ◽

Sequencing Technology ◽

Autonomous Region

Four mine contaminated soils located in northwest of Guangxi autonomous region were selected for microbial community analysis. These mine soils were contaminated by chromium (Cr) and cadmium (Cd). Microbial communities were described by high-throughput sequencing technology, which showed 39 different phyla in four samples. Among these phyla, Proteobacteria was the most abundant phylum in all samples. Acidobacteria, Actinobacteria, Planctomycetes, Firmicutes, Gemmatimonadetes, Bacteroidetes and Chloroflexi showed higher relative abundances than other phyla. In addition, a wide diversity of bacteria with the potential of bioremediation, such as Sphingomonas, Lysobacter and Gemmatimonas were detected in the tested mine contaminated soils. The results of microbial community analysis will provide a new target for isolation of microorganisms with the potential of bioremediation and lay the foundation for a great enhancement of bioremediation ability through the genetic engineering modification of indigenous microorganisms in future.

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