Homogenization of Rhizosphere Bacterial Communities by Pea (Pisum sativum L.) Cultivated under Different Conservation Agricultural Practices in the Eastern Himalayas

AbstractConservation agriculture offers a suitable system to harmonize agriculture with the environment, especially in fragile ecosystems of North-East India. Soil microbes play pivotal roles in ecosystem functioning and act as indispensable indicators of overall fitness of crop plant and soil health. Here we demonstrated that altercations in residue management and tillage practices lead to the development of differential bacterial communities forcing the pea plants to recruit special groups of bacteria leading to highly homogenous rhizosphere communities. Pea rhizosphere and bulk soil samples were collected, and bacterial community structure was estimated by 16S rRNA gene amplicon sequencing and predictive functional analysis was performed using Tax4Fun. The effect on pea plants was evident in the bacterial communities as the overall diversity of rhizosphere samples was significantly higher to that of bulk soil samples. Bacillus, Staphylococcus, Planomicrobium, Enterobacter, Arthrobacter, Nitrobacter, Geobacter, and Sphingomonas were noticed as the most abundant genera in the rhizosphere and bulk soil samples. The abundance of Firmicutes and Proteobacteria altered significantly in the rhizosphere and bulk samples, which was further validated by qPCR. Selection of specific taxa by pea plant was indicated by the higher values of mean proportion of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter and Sphingomonas in rhizosphere samples, and Massilia, Paenibacillus and Planomicrobium in bulk soil samples. Tillage and residue management treatments did not significantly alter the bacterial diversity, while their influence was observed on the abundance of few genera. Recorded results revealed that pea plant selects specific taxa into its rhizosphere plausibly to meet its requirements for nutrient uptake and stress amelioration under the different tillage and residue management practices.

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Unravelling the composition of soil belowground microbial community before sowing transgenic cotton

Plant Soil and Environment ◽

10.17221/523/2017-pse ◽

2017 ◽

Vol 63 (No. 11) ◽

pp. 512-518

Author(s):

Vital Lourdes ◽

Narvaez Jose A ◽

Cruz Maria Antonia ◽

Ortiz Eyra L ◽

Sanchez Eric ◽

...

Keyword(s):

Bacterial Communities ◽

Chemical Properties ◽

Alpha Diversity ◽

Soil Samples ◽

Bulk Soil ◽

Personal Genome ◽

Transgenic Crop ◽

Rrna Gene ◽

Sequencing Analysis ◽

Ion Torrent Pgm

Soils harbour enormously diverse bacterial communities that interact specifically with plants generating beneficial interactions between them. This study was the first approach to assess bacterial communities before sowing with three cotton genotypes, including both transgenic and conventional ones. The structure of bacterial communities was identified using the next generation sequencing analysis, ion torrent PGM (Personal Genome Machine™) sequencer technology, based on the V2–V3 16S rRNA gene region. Quantitative insights into microbial ecology pipeline were used to identify the structure and diversity of bacterial communities in bulk soil samples collected in the northeast of Mexico. Bulk soil textures and chemical properties, including most nutrients, were homogeneous in these bulk soil samples. Relative abundance analysis showed similar bacterial community structures. Dominant taxonomic phyla were Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria, Gemmatimonadetes and Bacteroidetes, whereas the main families were Bacillaceae, Chitinophagaceae and Rhodospirillaceae with an abundance average of BS1 (bulk soil sample), BS2 and BS3 (24.85, 19.74 and 19.71%, respectively). Alpha diversity analysis showed a high diversity (Shannon and Simpson index) and a large value of the observed species found in bulk soils samples. These results allowed establishing the previous bacterial structural community in an unused soil before sowing it with a transgenic crop for the first time.

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Impacts of switching tillage to no-tillage and vice versa on soil structure, enzyme activities, and prokaryotic community profiles in Argentinean semi-arid soils

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab025 ◽

2021 ◽

Author(s):

L A Gabbarini ◽

E Figuerola ◽

J P Frene ◽

N B Robledo ◽

F M Ibarbalz ◽

...

Keyword(s):

Community Structure ◽

Soil Structure ◽

Management Practices ◽

Soil Health ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Prokaryotic Community ◽

C Cycle

Abstract The effects of tillage on soil structure, physiology, and microbiota structure were studied in a long-term field experiment, with side-to-side plots, established to compare effects of conventional tillage (CT) vs. no-till (NT) agriculture. After 27 years, part of the field under CT was switched to NT and vice versa. Soil texture, soil enzymatic profiles, and the prokaryotic community structure (16S rRNA genes amplicon sequencing) were analysed at two soil depths (0–5, 5–10 cm) in samples taken 6, 18, and 30 months after switching tillage practices. Soil enzymatic activities were higher in NT than CT, and enzymatic profiles responded to the changes much earlier than the overall prokaryotic community structure. Beta diversity measurements of the prokaryotic community indicated that the levels of stratification observed in long-term NT soils were already recovered in the new NT soils thirty months after switching from CT to NT. Bacteria and Archaea OTUs, which responded to NT were associated with coarse soil fraction, SOC and C cycle enzymes while CT responders were related to fine soil fractions and S cycle enzymes. This study showed the potential of managing the soil prokaryotic community and soil health through changes in agricultural management practices.

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Soil aggregate-based nucleic acid analyses of the impact of maize roots and their root hairs on the structural diversity of microbial communities

10.5194/egusphere-egu21-7620 ◽

2021 ◽

Author(s):

Christoph Tebbe ◽

Damini Damini ◽

Damien Finn ◽

Nataliya Bilyera ◽

Minh Ganther ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Root Hair ◽

Soil Aggregates ◽

Root Hairs ◽

Soil Samples ◽

Plant Roots ◽

Bulk Soil ◽

Rrna Gene ◽

The Impact

The deposition of energy rich carbon sources released by plant roots during their growth fuels microbially driven ecosystem processes in soil, but there is a lack of understanding how microorganisms interact and collaborate. The objective of this research was therefore to characterize microbial networks as they assemble under the influence of plant roots. To identify the specific importance of root hairs, we compared the impact of a maize wild-type to a root-air defective mutant (rth3; (1).The microbial community structure was analyzed by qPCR and 16S rRNA gene amplicon sequencing from soil DNA. In order to increase the probability of detecting truly interacting microbial partners as a basis for network analyses, we first evaluated a new protocol to obtain DNA from as little as 1 mg instead of the usual 250 mg soil samples, thereby approaching the aggregate level (2). While the diversity of bacterial 16S rRNA gene amplicons of 250-mg samples taken from the same soil was not distinct, DNA analyses from individual aggregates clearly differed from each other underlining that soil aggregates represent distinct microbial habitats.Soil column experiments with maize grown in a loam soil (3) revealed distinct communities between rhizosphere and bulk soil. The community composition of individual aggregates showed more differences in bulk soil compared to rhizosphere. Less elaborated networks were seen in bulk soil and a profound effect of root hairs could be unravelled. Null model testing demonstrated that Actinobacteria were equally important for network connectivity independent of the root hair mutation, but for networks of the wildtype, Acidobacteria were essential for synergistic interactions and overall network structure. In contrast, Proteobacteria and Firmicutes connectivity became more important. The observed differences in community composition and interactions suggests carbon cycling, and perhaps other microbially-driven functions, are markedly affected by the presence of root hairs.Utilizing maize root soil microcosms for studying soil zymography in the rhizosphere allowed to obtain soil samples from regions with distinct specific enzyme activities. In order to enhance the detection of actively metabolizing bacterial community members, we studied rRNA sequences and compared it to rRNA gene sequences from the same samples. Currently the data are under analysis.References(1) Wen, T-J, Schnable PS (1994) Analyses of mutants of three genes that influence root hair development in Zea mays (Gramineae) suggest that root hairs are dispensable. Am. J. Bot. 81, 833&#8211;842.(2) Szoboszlay M, Tebbe CC (2020) Hidden heterogeneity and co-occurrence networks of soil prokaryotic communities revealed at the scale of individual soil aggregates. Microbiol. Open, e1144. DOI: 10.1002/mbo3.1144(3) Vetterlein D et al. (2020) Experimental platforms for the investigation of spatiotemporal patterns in the rhizosphere &#8211; laboratory and field scale. J. Plant Nutr. Soil Sci., 000, 1&#8211;16 DOI: 10.1002/jpln.202000079

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Paddy Soil Profile Distribution of δ13C Subjected to Rice Straw Amendment and Burning

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.886.3 ◽

2019 ◽

Vol 886 ◽

pp. 3-7 ◽

Cited By ~ 1

Author(s):

Wutthikrai Kulsawat ◽

Boonsom Porntepkasemsan ◽

Phatchada Nochit

Keyword(s):

Organic Carbon ◽

Paddy Soil ◽

Soil Profile ◽

Management Practices ◽

Soil Depth ◽

Animal Health ◽

Soil Samples ◽

Residue Management ◽

Straw Amendment ◽

Stubble Burning

Paddy residues are the most generous agricultural biomass from the paddy cultivation, Paddy residues practices include crop residue amendment and in-situ burning. It indicated that residue amendment increased the organic carbon and nutrient contents in soil, However, an open residue burning is still a common practice in Thailand despite of strict law enforcements and proper education to farmers about its implications on soil, human and animal health The present study determined how residues management practices: residue amendment and stubble burning, influence the soil organic carbon by determining δ13C in paddy soil profile. The 30 cm depth soil samples from the naturally straw amendment and stubble burning paddy fields were collected in Chiang Khwan district, Roi-et province during 2017. The δ13C values with soil depth showed that residue management practices produce statistical differences in both soils. The δ13C values of soil samples from amendment and burning sites ranged from-23.19‰ to-17.98‰ and-24.79‰ to-19.28‰, respectively. Carbon isotopes differentiate clearly between amendment site (more positive values) and burning site (more negative values). The results from this study were in accordance with literatures which reported that the δ13C distribution in the soil profile can be applied to study in SOC dynamics as a result of different paddy residue management practices (amendment or burning). Further research is needed to confirm the validity of the stable carbon isotope technique in this type of studies.

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Gut microbiota composition is associated with narcolepsy type 1

Neurology Neuroimmunology & Neuroinflammation ◽

10.1212/nxi.0000000000000896 ◽

2020 ◽

Vol 7 (6) ◽

pp. e896

Author(s):

Alexandre Lecomte ◽

Lucie Barateau ◽

Pedro Pereira ◽

Lars Paulin ◽

Petri Auvinen ◽

...

Keyword(s):

Community Structure ◽

Gut Microbiota ◽

Bacterial Communities ◽

Beta Diversity ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Differential Abundance ◽

Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

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The Wheat Microbiome Under Four Management Strategies, and Potential for Endophytes in Disease Protection

Phytobiomes Journal ◽

10.1094/pbiomes-05-17-0023-r ◽

2017 ◽

Vol 1 (3) ◽

pp. 158-168 ◽

Cited By ~ 51

Author(s):

Kristi Gdanetz ◽

Frances Trail

Keyword(s):

Bacterial Communities ◽

Management Strategy ◽

Crop Yields ◽

Management Strategies ◽

Growing Season ◽

Amplicon Sequencing ◽

Antagonistic Activity ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Plant Organ

Manipulating plant-associated microbes to reduce disease or improve crop yields requires a thorough understanding of interactions within the phytobiome. Plants were sampled from a wheat/maize/soybean crop rotation site that implements four different crop management strategies. We analyzed the fungal and bacterial communities of leaves, stems, and roots of wheat throughout the growing season using 16S and fungal internal transcribed spacer 2 rRNA gene amplicon sequencing. The most prevalent operational taxonomic units (OTUs) were shared across all samples, although levels of the low-abundance OTUs varied. Endophytes were isolated from plants, and tested for antagonistic activity toward the wheat pathogen Fusarium graminearum. Antagonistic strains were assessed for plant protective activity in seedling assays. Our results suggest that microbial communities were strongly affected by plant organ and plant age, and may be influenced by management strategy.

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Temporal variation in soil bacterial communities can be confounded with spatial variation

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa192 ◽

2020 ◽

Vol 96 (12) ◽

Author(s):

Syrie M Hermans ◽

Hannah L Buckley ◽

Fiona Curran-Cournane ◽

Matthew Taylor ◽

Gavin Lear

Keyword(s):

Temporal Variation ◽

Bacterial Communities ◽

Amplicon Sequencing ◽

Spatial Distance ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Causal Processes ◽

Fundamental Understanding ◽

Soil Bacterial ◽

Indigenous Forest

ABSTRACT Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period. Temporal variation appeared to be greater when fewer spatial samples per site were analysed, as well as in human-impacted compared to indigenous sites (P < 0.01 for both). The biggest portion of variation in bacterial community richness and composition was explained by soil physicochemical variables (13–24%) rather than spatial distance or sampling time (<1%). These results highlight the importance of adequate spatiotemporal replication when sampling soil communities for environmental monitoring, and the importance of conducting temporal research across a wide variety of land uses. This will ensure we have a true understanding of how bacterial communities change over space and time; the work presented here provides important considerations for how such research should be designed.

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Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish

FEMS Microbiology Ecology ◽

10.1093/femsec/fiz179 ◽

2019 ◽

Author(s):

Lara Parata ◽

Shaun Nielsen ◽

Xing Xing ◽

Torsten Thomas ◽

Suhelen Egan ◽

...

Keyword(s):

Coral Reef ◽

Gastrointestinal Tract ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Communities ◽

Food Source ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Bacterial Symbionts ◽

Adult Fish

Abstract Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.

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Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

10.21203/rs.3.rs-384378/v1 ◽

2021 ◽

Author(s):

Nicole E Adams ◽

Madeleine A Becker ◽

Suzanne Edmands

Keyword(s):

Bacterial Diversity ◽

Bacterial Communities ◽

Captive Breeding ◽

Interdisciplinary Approach ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Sample Collection ◽

Channel Island ◽

Island Fox ◽

Urocyon Littoralis

Abstract Background With developing understanding that host-associated microbiota play significant roles in individual health and fitness, taking an interdisciplinary approach combining microbiome research with conservation science is increasingly favored. Here we establish the scat microbiome of the imperiled Channel Island fox (Urocyon littoralis) and look at the effects of geography and captivity on the variation in bacterial communities. Results Using high throughput 16S rRNA gene amplicon sequencing, we discovered distinct bacterial communities in each island fox subspecies. Weight, timing of the sample collection, and sex contributed to the geographic patterns. We uncovered significant taxonomic differences and an overall decrease in bacterial diversity in captive versus wild foxes. Conclusions Understanding the drivers of microbial variation in this system provides a valuable lens through which to evaluate the health and conservation of these genetically depauperate foxes. The island-specific bacterial community baselines established in this study can make monitoring island fox health easier and understanding the implications of inter-island translocation clearer. The decrease in bacterial diversity within captive foxes could lead to losses in the functional services normally provided by commensal microbes and suggests that zoos and captive breeding programs would benefit from maintaining microbial diversity.

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Press xenobiotic disturbance favors deterministic assembly with a shift in function and structure of bacterial communities in sludge bioreactors

10.1101/2020.10.15.341966 ◽

2020 ◽

Author(s):

Ezequiel Santillan ◽

Hari Seshan ◽

Stefan Wuertz

Keyword(s):

Community Structure ◽

Bacterial Communities ◽

Temporal Dynamics ◽

Treatment Plant ◽

Amplicon Sequencing ◽

Rrna Gene ◽

Batch Reactors ◽

Function Structure ◽

Community Function ◽

And Function

AbstractDisturbance is thought to affect community assembly mechanisms, which in turn shape community structure and the overall function of the ecosystem. Here, we tested the effect of a continuous (press) xenobiotic disturbance on the function, structure, and assembly of bacterial communities within a wastewater treatment system. Two sets of four-liter sequencing batch reactors were operated in triplicate with and without the addition of 3-chloroaniline for a period of 132 days, following 58 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of bacterial community structure were derived from 16S rRNA gene amplicon sequencing. Community function, structure and assembly differed between press disturbed and undisturbed reactors. Temporal partitioning of assembly mechanisms via phylogenetic and non-phylogenetic null modelling analysis revealed that deterministic assembly prevailed for disturbed bioreactors, while the role of stochastic assembly was stronger for undisturbed reactors. Our findings are relevant because research spanning various disturbance types, environments and spatiotemporal scales is needed for a comprehensive understanding of the effects of press disturbances on assembly mechanisms, structure, and function of microbial communities.Graphical abstract

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