scholarly journals Enriched root bacterial microbiome in invaded vs native ranges of the model grass allotetraploid Brachypodium hybridum

2021 ◽  
Author(s):  
Brooke Pickett ◽  
Chelsea J. Carey ◽  
Keshav Arogyaswamy ◽  
Jon Botthoff ◽  
Mia Maltz ◽  
...  
Keyword(s):  
Brachypodium Distachyon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Biotic Interactions ◽  
Plant Invasions ◽  
Amplicon Sequencing ◽  
Microbial Interactions ◽  
Bioenergy Crops ◽  
Native Range ◽  
Soil Microbial

AbstractInvasive species can shift the composition of key soil microbial groups, thus creating novel soil microbial communities. To better understand the biological drivers of invasion, we studied plant-microbial interactions in species of the Brachypodium distachyon complex, a model system for functional genomic studies of temperate grasses and bioenergy crops. While Brachypodium hybridum invasion in California is in an incipient stage, threatening natural and agricultural systems, its diploid progenitor species B. distachyon is not invasive in California. We investigated the root, soil, and rhizosphere bacterial composition of Brachypodium hybridum in both its native and invaded range, and of B. distachyon in the native range. We used high-throughput, amplicon sequencing to evaluate if the bacteria associated with these plants differ, and whether biotic controls may be driving B. hybridum invasion. Bacterial community composition of B. hybridum differed based on provenance (native or invaded range) for root, rhizosphere, and bulk soils, as did the abundance of dominant bacterial taxa. Bacteroidetes, Cyanobacteria and Bacillus spp. (species) were significantly more abundant in B. hybridum roots from the invaded range, whereas Proteobacteria, Firmicutes, Erwinia and Pseudomonas were more abundant in the native range roots. Brachypodium hybridum forms novel biotic interactions with a diverse suite of rhizosphere microbes from the invaded range, which may not exert a similar influence within its native range, ostensibly contributing to B. hybridum’s invasiveness. These associated plant microbiomes could inform future management approaches for B. hybridum in its invaded range and could be key to understanding, predicting, and preventing future plant invasions.

scholarly journals Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes1

2019 ◽  
Vol 97 (11) ◽  
pp. 4567-4578 ◽  
Author(s):  
Margaret D Weinroth ◽  
Jennifer N Martin ◽  
Enrique Doster ◽  
Ifigenia Geornaras ◽  
Jennifer K Parker ◽  
...  
Keyword(s):  
Liver Abscess ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Feedlot Cattle ◽  
Microbiome Composition ◽  
Soil Microbial ◽  
16S Rrna Amplicon Sequencing ◽  
Liver Abscesses ◽  
Geographical Regions ◽  
Antimicrobial Resistance Genes

Abstract Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in 3 geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from 3 geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin-administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes, but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.

scholarly journals Biological H2 and CO oxidation activities are sensitive to compositional change of soil microbial communities

2020 ◽  
Vol 66 (4) ◽  
pp. 263-273
Author(s):  
Julien Saavedra-Lavoie ◽  
Anne de la Porte ◽  
Sarah Piché-Choquette ◽  
Claude Guertin ◽  
Philippe Constant
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Co Oxidation ◽  
Soil Microbial Communities ◽  
Amplicon Sequencing ◽  
Oxidative Capacity ◽  
Rrna Gene ◽  
Soil Microbial Diversity ◽  
Soil Microcosms ◽  
Soil Microbial

Trace gas uptake by microorganisms controls the oxidative capacity of the troposphere, but little is known about how this important function is affected by changes in soil microbial diversity. This article bridges that knowledge gap by examining the response of the microbial community-level physiological profiles (CLPPs), carbon dioxide (CO2) production, and molecular hydrogen (H2) and carbon monoxide (CO) oxidation activities to manipulation of microbial diversity in soil microcosms. Microbial diversity was manipulated by mixing nonsterile and sterile soil with and without the addition of antibiotics. Nonsterile soil without antibiotics was used as a reference. Species composition changed significantly in soil microcosms as a result of dilution and antibiotic treatments, but there was no difference in species richness, according to PCR amplicon sequencing of the bacterial 16S rRNA gene. The CLPP was 15% higher in all dilution and antibiotic treatments than in reference microcosms, but the dilution treatment had no effect on CO2 production. Soil microcosms with dilution treatments had 58%–98% less H2 oxidation and 54%–99% lower CO oxidation, relative to reference microcosms, but did not differ among the antibiotic treatments. These results indicate that H2 and CO oxidation activities respond to compositional changes of microbial community in soil.

scholarly journals Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Kateryna Zhalnina ◽  
Karsten Zengler ◽  
Dianne Newman ◽  
Trent R. Northen
Keyword(s):  
Microbial Communities ◽  
Metabolic Networks ◽  
Soil Microbial Communities ◽  
Microbial Interactions ◽  
Microbial Consortia ◽  
Cellular Biology ◽  
Model Organisms ◽  
Soil Microbial ◽  
Integrative Framework ◽  
Genome Annotations

ABSTRACTThe chemistry underpinning microbial interactions provides an integrative framework for linking the activities of individual microbes, microbial communities, plants, and their environments. Currently, we know very little about the functions of genes and metabolites within these communities because genome annotations and functions are derived from the minority of microbes that have been propagated in the laboratory. Yet the diversity, complexity, inaccessibility, and irreproducibility of native microbial consortia limit our ability to interpret chemical signaling and map metabolic networks. In this perspective, we contend that standardized laboratory ecosystems are needed to dissect the chemistry of soil microbiomes. We argue that dissemination and application of standardized laboratory ecosystems will be transformative for the field, much like how model organisms have played critical roles in advancing biochemistry and molecular and cellular biology. Community consensus on fabricated ecosystems (“EcoFABs”) along with protocols and data standards will integrate efforts and enable rapid improvements in our understanding of the biochemical ecology of microbial communities.

scholarly journals Effects of Wildfire and Harvest Disturbances on Forest Soil Bacterial Communities

2007 ◽  
Vol 74 (1) ◽  
pp. 216-224 ◽  
Author(s):  
Nancy R. Smith ◽  
Barbara E. Kishchuk ◽  
William W. Mohn
Keyword(s):  
Microbial Biomass ◽  
Microbial Communities ◽  
Community Composition ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Microbial Biomass Carbon ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Microbial Biomass Nitrogen ◽  
Soil Microbial

ABSTRACT Wildfires and harvesting are important disturbances to forest ecosystems, but their effects on soil microbial communities are not well characterized and have not previously been compared directly. This study was conducted at sites with similar soil, climatic, and other properties in a spruce-dominated boreal forest near Chisholm, Alberta, Canada. Soil microbial communities were assessed following four treatments: control, harvest, burn, and burn plus timber salvage (burn-salvage). Burn treatments were at sites affected by a large wildfire in May 2001, and the communities were sampled 1 year after the fire. Microbial biomass carbon decreased 18%, 74%, and 53% in the harvest, burn, and burn-salvage treatments, respectively. Microbial biomass nitrogen decreased 25% in the harvest treatment, but increased in the burn treatments, probably because of microbial assimilation of the increased amounts of available NH4 + and NO3 − due to burning. Bacterial community composition was analyzed by nonparametric ordination of molecular fingerprint data of 119 samples from both ribosomal intergenic spacer analysis (RISA) and rRNA gene denaturing gradient gel electrophoresis. On the basis of multiresponse permutation procedures, community composition was significantly different among all treatments, with the greatest differences between the two burned treatments versus the two unburned treatments. The sequencing of DNA bands from RISA fingerprints revealed distinct distributions of bacterial divisions among the treatments. Gamma- and Alphaproteobacteria were highly characteristic of the unburned treatments, while Betaproteobacteria and members of Bacillus were highly characteristic of the burned treatments. Wildfire had distinct and more pronounced effects on the soil microbial community than did harvesting.

scholarly journals Micro-aggregation of a pristine grassland soil selects for bacterial and fungal communities and changes in nitrogen cycling potentials

2021 ◽  
Author(s):  
Christoph Keuschnig ◽  
Jean Martins ◽  
Aline Navel ◽  
Pascal Simonet ◽  
Catherine Larose
Keyword(s):  
Particle Size ◽  
Nitrogen Cycling ◽  
Bacterial Communities ◽  
Soil Microbial Communities ◽  
Microbial Interactions ◽  
Fungal Communities ◽  
Supernatant Fraction ◽  
Soil Microbial ◽  
Microbial Analysis

Microbial analysis at the micro scale of soil is essential to the overall understanding of microbial organization and interactions, and necessary for a better understanding of soil ecosystem functioning. While bacterial communities have been extensively described, little is known about the organization of fungal communities as well as functional potentials at scales relevant to microbial interactions. Fungal and bacterial communities and changes in nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size sub-fractions (PSFs; > 250 µm, 250-63 µm, 63-20 µm, 20-2 µm, < 2 µm and supernatant) were studied. The potential for nitrogen reduction was found elevated in bigger aggregates. The relative abundance of Basidiomycota deceased with decreasing particle size, Ascomycota showed an increase and Mucoromycota became more prominent in particles less than 20 µm. Bacterial community structures changed below 20 µm at the scale where microbes operate.Strikingly, only members of two bacterial and one fungal phyla (Proteobacteria, Bacteroidota and Ascomycota, respectively) were washed-off the soil during fractionation and accumulated in the supernatant fraction where most of the detected bacterial genera (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium and Variovorax) were previously associated with exopolysaccharide production and biofilm formation.Overall, the applied method shows potential to study soil microbial communities at micro scales which might be useful in studies focusing on the role of specific fungal taxa in soil structure formation as well as research on how and by whom biofilm-like structures are distributed and organized in soil.

scholarly journals The Coexistence Relationship Between Plants and Soil Bacteria Based on Interdomain Ecological Network Analysis

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Cong ◽  
Jingjing Yu ◽  
Kai Feng ◽  
Ye Deng ◽  
Yuguang Zhang
Keyword(s):  
Soil Bacteria ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Soil Microbial ◽  
Microbial Group ◽  
Below Ground ◽  
Complex Relationships ◽  
And Function ◽  
The Relationship ◽  
Warm Temperate

The relationship between plants and their associated soil microbial communities plays a crucial role in maintaining ecosystem processes and function. However, identifying these complex relationships is challenging. In this study, we constructed an interdomain ecology network (IDEN) of plant–bacteria based on SparCC pairwise associations using synchronous aboveground plant surveys and belowground microbial 16S rRNA sequencing among four different natural forest types along the climate zones in China. The results found that a total of 48 plants were associated with soil bacteria among these four sites, and soil microbial group associations with specific plant species existed within the observed plant–bacteria coexistence network. Only 0.54% of operational taxonomy units (OTUs) was shared by the four sites, and the proportion of unique OTUs for each site ranged from 43.08 to 76.28%, which occupied a large proportion of soil bacterial community composition. The plant–bacteria network had a distinct modular structure (p &lt; 0.001). The tree Acer tetramerum was identified as the network hubs in the warm temperate coniferous and broad-leaved mixed forests coexistence network and indicates that it may play a key role in stabilizing of the community structure of these forest ecosystems. Therefore, IDEN of plant–bacteria provides a novel perspective for exploring the relationships of interdomain species, and this study provides valuable insights into understanding coexistence between above-ground plants and below-ground microorganisms.

Five years of experimental summer drought – Anatomical and physiological acclimation of mature beech and spruce

2020 ◽  
Author(s):  
Thorsten Grams
Keyword(s):  
Norway Spruce ◽  
Soluble Sugars ◽  
Soil Microbial Communities ◽  
European Beech ◽  
Microbial Interactions ◽  
Rooting Depth ◽  
Summer Drought ◽  
Soil Microbial ◽  
Roof Experiment ◽  
Whole Tree

&lt;p&gt;This contribution summarizes the outcome of a five-year experiment on mature (60-80 years old) trees in a Central European forest. We studied roughly 100 trees of European beech and Norway spruce, two tree species of contrasting foliage (i.e. deciduous vs. evergreen) and stomatal sensitivity to drought (i.e. anisohydric vs. isohydric behavior). Trees were exposed to experimentally induced summer droughts from 2014 to 2018 with precipitation throughfall being completely excluded during the growing seasons. The throughfall-exclusion study was established on 12 plots with trees readily accessible by canopy crane (Kranzberg forest roof experiment, southern Germany). We aimed at bringing trees to the edge of survival to studying trees&amp;#8217; capability for acclimation under repeated, severe summer droughts as expected more frequently in future climate scenarios. Results come from a multidisciplinary approach focusing on mechanisms of acclimation, eventually reducing trees&amp;#8217; vulnerability to drought during the five-year study period. Presented data integrate responses from the level of soil/microbial interactions over tree organs and whole-tree morphology to responses at the stand level.&lt;/p&gt;&lt;p&gt;During the first two years, restrictions caused by drought were most prominent, exemplified by pre-dawn leaf water potentials of down to -2.5 MPa and reductions in photosynthesis and growth by up to 50 and 80 % in European beech and Norway spruce, respectively. Nevertheless, percentage loss of conductivity in branch xylem was hardly affected. Likewise, concentrations of non-structural carbohydrates (sum of soluble sugars and starch) in tree organs remained largely unaffected, but translated to significantly lower carbohydrate pool sizes in view of strongly reduced tree growth. Nevertheless, two spruce trees died from drought, in the absence of bark beetle or pathogen interactions. During the fourth and fifth year of summer drought, trees showed clear signs of drought acclimation with e.g. some recovery of stomatal conductance, reductions of whole-tree leaf area, changes in rooting depth and acclimation of associated soil microbial communities. Accordingly, stem diameter growth recovered during the last years of the stress treatment, indicating reduced vulnerability of trees towards the end of the five-year drought treatment.&lt;/p&gt;

scholarly journals Urbanization-induced environmental changes strongly affect wetland soil bacterial community composition and diversity

2021 ◽  
Author(s):  
Xinyu Yi ◽  
Chen Ning ◽  
Shuailong Feng ◽  
Haiqiang Gao ◽  
Jianlun Zhao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Soil Microbial Communities ◽  
Environmental Drivers ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Soil Microbial ◽  
Soil Bacterial

Abstract Soil microbial communities potentially serve as indicators for their responses to changes in various ecosystems at scales from a region to the globe. However, changes in wetland soil bacterial communities and how they are related to urbanization intensities remains poorly understood. Here, we collected sixty soil samples along urbanization intensity gradients from twenty wetlands. We measured a range of environmental factors and characterized bacterial communities structure using 16S rRNA gene amplicon sequencing that targeted the V4-V5 region. Our results revealed the dominant soil microbial phyla included Proteobacteria (39.3%), Acidobacteria (21.4%) and Chloroflexi (12.3%) in the wetlands, and showed a significant divergence of composition in intensive urbanization area (UI_4) than other places. A critical "threshold" exists in the soil bacterial diversity, demonstrating different patterns: a gradual increase in the areas of low-to-intermediate disturbances but a significant decrease in highly urbanized areas where metabolic functions were significantly strong. Additionally, soil pH, total phosphorus (TP), available phosphorus (AP ) and ammonia nitrogen (NH4+-N) made a significant contribution to variations in bacterial communities, explaining 49.6%, 35.1%, 26.2% and 30.7% of the total variance, respectively. pH and NH4+-N were identified as the main environmental drivers to determine bacterial community structure and diversity in the urban wetlands. Our results highlight collective changes in multiple environmental variables induced by urbanization rather than by the proportion of impervious surface area (ISA), which were potentially attributed to the spatial heterogeneity along different urbanization gradients.

Methylmercury production and degradation by soil microbial communities

2020 ◽  
Author(s):  
Yu-Rong Liu ◽  
Qiaoyun Huang
Keyword(s):  
Microbial Communities ◽  
Bacterial Community Composition ◽  
Inorganic Mercury ◽  
Soil Microbial Communities ◽  
Paddy Soils ◽  
Equation Modeling ◽  
Soil Microbial ◽  
Anaerobic Microorganisms ◽  
Water Saturated ◽  
Reducing Bacteria

&lt;p&gt;Rice consumption is now recognized as an important pathway of human exposure to the neurotoxin methylmercury (MeHg), particularly in countries where rice is a staple food. Although the discovery of a two-gene cluster hgcAB has linked Hg methylation to several phylogenetically diverse groups of anaerobic microorganisms converting inorganic mercury (Hg) to MeHg, the prevalence and diversity of microbial communities associated with MeHg production and degradation in paddy soils remain unclear. Both Illumina and PacBio sequencing analyses revealed that Hg methylating communities were dominated by iron-reducing bacteria (i.e., Geobacter) and methanogens, with a relatively low abundance of hgcA+ sulfate-reducing bacteria in the soil. A positive correlation was observed between the MeHg content in soil and the relative abundance of Geobacter carrying the hgcA gene. Our structure equation modeling suggested a much stronger link between bacterial community composition and %MeHg, compared to the abundance of methylating gene (hgcA) and edaphic properties. More importantly, random forest models suggested a more important role of non-Hg methylators than Hg methylators in predicting variations of soil %MeHg.&lt;/p&gt;&lt;p&gt;Microbial demethylation was demonstrated by significantly more degradation of MeHg in the unsterilized soils than the sterilized controls, although more degradation was observed in water-saturated soils than the unsaturated soil. 16S rRNA Illumina sequencing and metatranscriptomic analyses consistently revealed that Catenulisporaceae, Frankiaceae, Mycobacteriaceae, and Thermomonosporaceae were among the most likely microbial taxa in influencing These findings provide new insights into microbial communities associated with MeHg accumulation in paddy soils, with important implications in mitigating the net production and bioaccumulation of MeHg in rice worldwide.&lt;/p&gt;

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