Exploration of bacterial communities in products after composting rural wastes with different components: Core microbiome and potential pathogenicity

Abstract Background and aimsMany plant species grow better in sterilized than in live soil. Foliar application of SA mitigates this negative effect of live soil on the growth of the plant Jacobaea vulgaris. To examine what causes the positive effect of SA application on plant growth in live soils, we analyzed the effects of SA application on the composition of active rhizosphere bacteria in the live soil. Methods We studied this over four consecutive plant cycles (generations), using mRNA sequencing of the microbial communities in the rhizosphere of J. vulgaris. ResultsOur study shows that the composition of the rhizosphere bacterial communities of J. vulgaris greatly differed among generations. Application of SA resulted in both increases and decreases in a number of active bacterial genera in the rhizosphere soil, but the genera that were affected by the treatment differed among generations. In the first generation, there were no genera that were significantly affected by the SA treatment, indicating that induction of the SA defense pathway in plants does not lead to immediate changes in the soil microbial community. 89 species out of the total 270 (32.4%) were present in all generations in all soils of SA-treated and control plants suggesting that these make up the “core” microbiome. On average in each generation, 72.9% of all genera were present in both soils. Application of SA to plants significantly up-regulated genera of Caballeronia, unclassified Cytophagaceae, Crinalium and Candidatus Thermofonsia Clade 2, and down-regulated genera of Thermomicrobiales, unclassified Rhodobacterales, Paracoccus and Flavihumibacter. While the functions of many of these bacteria are poorly understood, bacteria of the genus Caballeronia play an important role in fixing nitrogen and promoting plant growth, and hence this suggests that activation of the SA signaling pathway in J. vulgaris plants may select for bacterial genera that are beneficial to the plant. ConclusionsOverall, our study shows that aboveground activation of defenses in the plant affects soil microbial communities and, as soil microbes can greatly influence plant performance, this implies that induction of plant defenses can lead to complex above-belowground feedbacks. Further studies should examine how activation of the SA signaling pathway in the plant changes the functional genes of the rhizosphere soil bacterial community.

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Seasonal Dynamics and Persistency of Endophyte Communities in Kalidium schrenkianum Shifts Under Radiation Stress

Frontiers in Microbiology ◽

10.3389/fmicb.2021.778327 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jing Zhu ◽

Xiang Sun ◽

Qi-Yong Tang ◽

Zhi-Dong Zhang

Keyword(s):

Microbial Community ◽

Community Composition ◽

Bacterial Communities ◽

Community Dynamics ◽

Microbial Community Composition ◽

Northwest China ◽

Community Diversity ◽

Radiation Stress ◽

Core Microbiome ◽

Essential Components

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.

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Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System

Frontiers in Microbiology ◽

10.3389/fmicb.2021.709611 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yousri Abdelhafiz ◽

Jorge M. O. Fernandes ◽

Simone Larger ◽

Davide Albanese ◽

Claudio Donati ◽

...

Keyword(s):

Bacterial Communities ◽

Nile Tilapia ◽

16S Rrna Gene Sequencing ◽

Study Groups ◽

Breeding Strategy ◽

Rrna Gene ◽

Beneficial Bacteria ◽

Core Microbiome ◽

Recirculating Aquaculture ◽

Opportunistic Bacteria

In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

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16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates

PeerJ ◽

10.7717/peerj.8417 ◽

2020 ◽

Vol 8 ◽

pp. e8417 ◽

Cited By ~ 2

Author(s):

Qiang Chen ◽

William A. Meyer ◽

Qiuwei Zhang ◽

James F. White

Keyword(s):

Microbial Community ◽

Seed Germination ◽

Bacterial Community ◽

16S Rrna ◽

Seedling Growth ◽

Bacterial Communities ◽

Metagenomic Analysis ◽

High Moisture ◽

Core Microbiome ◽

Dry Climates

Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea (12%) and Pseudomonas (11%) were the major genera in the bacterial communities regardless of climate conditions. Massilia, Pantoea and Pseudomonas dominated LM seeds, while Pedobacter and Sphingomonas dominated HM seeds. The species of turf seeds did not appear to influence bacterial community composition. The seeds of the three turf species showed a core microbiome consisting of 27 genera from phyla Actinobacteria, Bacteroidetes, Patescibacteria and Proteobacteria. Differences in seed-vectored microbes, in terms of diversity and density between high and LM climates, may result from effects of moisture level on the colonization of microbes and the development of microbe community on seed surface tissues (adherent paleas and lemmas). The greater diversity and density of seed vectored microbes in HM climates may benefit seedlings by helping them tolerate stress and fight disease organisms, but this dense microbial community may also compete with seedlings for nutrients, slowing or modulating seed germination and seedling growth.

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Metagenomics of a nickel-resistant bacterial community in an anthropogenic nickel-contaminated soil in southwest Slovakia

Biologia ◽

10.1515/biolog-2017-0117 ◽

2017 ◽

Vol 72 (9) ◽

Cited By ~ 2

Author(s):

Matej Remenár ◽

Jana Harichová ◽

Marcel Zámocký ◽

Domenico Pangallo ◽

Tomáš Szemes ◽

...

Keyword(s):

Bacterial Communities ◽

Core Microbiome ◽

The Core ◽

Microbial Assemblage ◽

Core Set ◽

Two Samples ◽

High Nickel ◽

Curtis Dissimilarity ◽

Contaminated Waste ◽

Disturbed Environment

AbstractThe sampling sites situated in southwest Slovakia are according to environmental monitoring of Slovakia a part of strongly disturbed environment by heavy metals, mainly by high nickel concentrations. The aim of the present study was to characterise a complete microbial assemblage from a dump containing heavy-metal-contaminated waste as well as from farmland situated nearby this dump by using shotgun sequencing of 16S rDNA amplicons. It was found that nickel influenced both species richness and diversity and that microbiota of both samples differed significantly (Bray-Curtis dissimilarity 0.73) at genus level mainly by abundances of sequences from particular genera and occurrences of the unique genera in individual bacterial communities. In spite of these differences between microbial assemblages, both samples shared many bacterial genera that might constitute the specific nickel-resistant bacterial niche, and it was possible to delineate the core microbiome of our two samples at species level. The core set of 30 species, represented by the phyla Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Cyanobacteria, suggest that these species might form a “core microbiome” of the specific nickel-resistant bacterial niche.

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Biogeographical patterns in soil bacterial communities across the Arctic region

10.1101/655431 ◽

2019 ◽

Author(s):

Lucie A Malard ◽

Muhammad Zohaib Anwar ◽

Carsten S Jacobsen ◽

David A Pearce

Keyword(s):

Bacterial Communities ◽

Variation Partitioning ◽

Arctic Region ◽

The Arctic ◽

Alkaline Soils ◽

Core Microbiome ◽

Soil Bacterial Communities ◽

Arctic Soil ◽

Soil Bacterial ◽

The Impact

AbstractThe considerable microbial diversity of soils, their variety and key role in biogeochemical cycling has led to growing interest in their global distribution and the impact that environmental change might have at the regional level. In the broadest study of Arctic soil bacterial communities to date, we used high-throughput DNA sequencing to investigate the bacterial diversity from 200 independent Arctic soil samples from 43 sites. We quantified the impact of spatial and environmental factors on bacterial community structure using variation partitioning analysis, illustrating a non-random distribution across the region. pH was confirmed as the key environmental driver structuring Arctic soil bacterial communities, while total organic carbon, moisture and conductivity were shown to have little effect. Specialist taxa were more abundant in acidic and alkaline soils while generalist taxa were more abundant in acidoneutral soils. Of 48,147 bacterial taxa, a core microbiome composed of only 13 taxa that were ubiquitously distributed and present within 95% of samples was identified, illustrating the high potential for endemism in the region. Overall, our results demonstrate the importance of spatial and edaphic factors on the structure of Arctic soil bacterial communities.

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Large Rhizosphere Bacterial Diversity Exits Among Wild Progenitor Species of Modern Sugarcane (Saccharum Spp. Inter-Specific Hybrids)

10.21203/rs.3.rs-144226/v1 ◽

2021 ◽

Author(s):

Mukesh Kumar Malviya ◽

Chnag-Ning Li ◽

Manoj Kumar Solanki ◽

Prakash Lakshmanan ◽

Rajesh Kumar Singh ◽

...

Keyword(s):

Plant Growth ◽

Bacterial Diversity ◽

Bacterial Communities ◽

Wild Progenitor ◽

Core Microbiome ◽

Saccharum Spp ◽

Operational Taxonomic Units ◽

Plant Growth Promoting ◽

Related Wild Species ◽

Growth Promoting

Abstract BackgroundRhizosphere is rich in highly diverse and complex microbial communities. Plant growth promoting rhizpbacteria and diazotrops are played crucial role in plant growth and development. In this study, rhizosphere soils were collected from five wild Saccharum species- S. officinarum L. cv Badila (BRS), S. barberi Jesw. cv Pansahi (PRS), S. robustum (RRS), S. spontaneum (SRS), and S. sinense Roxb. cv Uba (URS) for studied of rhizosphere and diazotroph bacterial diversity using 16S rRNA and nifH gene amplification and sequencing.ResultsWe detected a total of 6202 operational taxonomic units (OTUs) specific to the bacterial communities from all species combined. Out of the 107 bacterial communities detected among all samples, we found a core microbiome of 31 rhizobacterial families spread across all the species analyzed. A total of 1099 OTUs were identified for diazotrophs with a core microbiome of 9 families distributed among all the sugarcane species. The core microbiomes were distributed across twenty genera-Bradyrhizobium, Dechloromonas, Desulfovibrio, Stenotrophomonas, Xanthobacter, Anaeromyxobacter, Azospirillum, Pseudoacidovorax, Methylobacterium, Azoarcus, Paenibacillus, Ideonella, Beijerinckia, Paraburkholderia, Burkholderia, Ruficoccus, Geobacter, Sinorhizobium, Kosakonia, and Azotobacter. ConclusionThe results presented here advance our understanding of rhizosphere associated bacterial diversity among genetically closely related wild species and provide a knowledge base for studying the evolution of rhizobacteria-host plant association during crop domestication.

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Microbiota Diversity in Pearl Oyster Pinctada fucata martensii Intestine and Its Aquaculture Environment

Frontiers in Marine Science ◽

10.3389/fmars.2021.655698 ◽

2021 ◽

Vol 8 ◽

Author(s):

Zhe Zheng ◽

Yongshan Liao ◽

Jianming Ye ◽

Chuangye Yang ◽

Linda Adzigbli ◽

...

Keyword(s):

Amino Acids ◽

Intestinal Microbiota ◽

Bacterial Communities ◽

Pearl Oyster ◽

Pinctada Fucata ◽

Sequencing Data ◽

Surrounding Water ◽

Core Microbiome ◽

Pearl Oysters ◽

Surrounding Seawater

Environmental microbiota plays a vital role in the intestinal microbiota of aquatic organisms. However, data concerning the association between the intestinal microbiota of pearl oyster Pinctada fucata martensii and the surrounding seawater are limited. The existing bacterial communities in pearl oyster intestine and surrounding water from two sites (D and H, within Liusha Bay in Guangdong, China) were investigated using 16S rRNA-based sequencing to explore the relationship among the two. D located in the inner bay, and H located in the open sea area outside bay. Results revealed the richness and diversity of pearl oyster intestinal microbiota to be less than those of the surrounding water, with 38 phyla and 272 genera observed as a result of the classifiable sequence. The microbiota compositions in the intestine and the surrounding water were diversified at the phylum and genus levels, with the sequencing data being statistically significant. However, the functional prediction of microbiota emphasized the overall similarity in the functional profile of the surrounding seawater and intestinal microbiomes. This profile was associated with metabolism of cofactors and vitamin, carbohydrates metabolism, amino acids metabolism, metabolism of terpenoids, and polyketides, metabolism of other amino acids, lipids metabolism, and energy metabolism. Seven common operational taxonomic units (OTUs), which belonged to phyla Tenericutes, Cyanobacteria, and Planctomycetes, were noted in the intestines of pearl oysters from two different sites. These OTUs may be affiliates to the core microbiome of pearl oyster. Significantly different bacterial taxa in the intestines of pearl oysters from two different sites were found at the phylum and genus levels. This finding suggested that the bacterial communities in pearl oyster intestines may exhibit some plasticity to adapt to changes in the surrounding water-cultured environment. This study generally offers constructive discoveries associated with pearl oyster intestinal microbiota and provides guidance for sustainable aquaculture.

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Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.03191-14 ◽

2014 ◽

Vol 81 (2) ◽

pp. 522-532 ◽

Cited By ~ 34

Author(s):

Wan-Ying Xie ◽

Jian-Qiang Su ◽

Yong-Guan Zhu

Keyword(s):

Bacterial Community ◽

Paddy Soil ◽

Bacterial Communities ◽

Bacterial Species ◽

Rrna Gene ◽

Core Microbiome ◽

Content Type ◽

Soil Ecosystems ◽

Α Diversity ◽

Floating Macrophytes

ABSTRACTThe phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We tookWolffia australianaas a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere ofW. australianaharbored considerably rich communities of bacteria, withProteobacteriaandBacteroidetesas the predominant phyla. The core microbiome in the phyllosphere contained genera such asAcidovorax,Asticcacaulis,Methylibium, andMethylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments.

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Unlocking the Microbiome Communities of Banana (Musa spp.) under Disease Stressed (Fusarium wilt) and Non-Stressed Conditions

Microorganisms ◽

10.3390/microorganisms8030443 ◽

2020 ◽

Vol 8 (3) ◽

pp. 443 ◽

Cited By ~ 2

Author(s):

Manoj Kaushal ◽

Rony Swennen ◽

George Mahuku

Keyword(s):

Fusarium Oxysporum ◽

Relative Abundance ◽

Fungal Community ◽

Bacterial Communities ◽

Fungal Communities ◽

Fungal Community Composition ◽

Core Microbiome ◽

Fungal Microbiota ◽

Diversity Structure ◽

Plant Components

We assessed the diversity, structure, and assemblage of bacterial and fungal communities associated with banana plants with and without Fusarium oxysporum f. sp. cubense (Foc) symptoms. A total of 117,814 bacterial and 17,317 fungal operational taxonomy units (OTUs) were identified in the rhizosphere, roots, and corm of the host plant. Results revealed that bacterial and fungal microbiota present in roots and corm primarily emanated from the rhizosphere. The composition of bacterial communities in the rhizosphere, roots, and corm were different, with more diversity observed in the rhizosphere and less in the corm. However, distinct sample types i.e., without (asymptomatic) and with (symptomatic) Fusarium symptoms were the major drivers of the fungal community composition. Considering the high relative abundance among samples, we identified core microbiomes with bacterial and fungal OTUs classified into 20 families and colonizing distinct plant components of banana. Our core microbiome assigned 129 bacterial and 37 fungal genera to known taxa.

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