Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

Abstract Background Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. Results In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. Conclusions We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

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Bacterial Composition and Diversity Associated with Rhizosphere of the Chinese Medicinal Herb Dendrobium

10.21203/rs.3.rs-58638/v1 ◽

2020 ◽

Author(s):

Yingdan Yuan ◽

Mengting Zu ◽

Lei Liu ◽

Xiaomei Song

Keyword(s):

Microbial Community ◽

Environmental Factor ◽

Bacterial Communities ◽

Soil Microorganisms ◽

Rhizosphere Soil ◽

Available Phosphorus ◽

Maturity Stage ◽

Bacterial Phyla ◽

Rhizosphere Microorganisms ◽

Rhizosphere Microbial Community

Abstract Background: Dendrobium is a precious herbal belongs to Orchid and widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most researches still focus on endophytes, and there is still large unknown in rhizosphere microorganisms. In order to investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during maturity stage of three kinds of Dendrobium species.Results: In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, Gemmatimonadetes. We analyzed the environmental factors of the growth of Dendrobium and found that the environmental factor that affects the rhizosphere soil microorganisms of Dendrobium is the soil factor. Among them, soil factors most closely related to the influence of Dendrobium rhizosphere soil microorganisms include total nitrogen, available phosphorus, ammonium nitrogen and pH value.Conclusions: We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, Bacteroidetes. Moreover, the smaller the level of bacterial, the greater the difference among Dendrobium species. Soil is the most important environmental factor affecting the bacterial communities in the rhizosphere soil of Dendrobium. These results fill the gap in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

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Effects of plant cultivars on the structure of bacterial and fungal communities associated with ginseng

10.21203/rs.3.rs-50235/v1 ◽

2020 ◽

Author(s):

Huaying Wang ◽

Xiaoxue Fang ◽

Hao Wu ◽

Xinyu Cai ◽

Hongxing Xiao

Keyword(s):

Microbial Community ◽

Bacterial Communities ◽

Fungal Diversity ◽

Microbial Community Composition ◽

Fungal Communities ◽

Associated Bacteria ◽

Rhizosphere Microorganisms ◽

Soil Rhizosphere ◽

Bacteria And Fungi ◽

Rhizosphere Microbial Community

Abstract Background There is a growing awareness of the importance of root-associated bacteria and fungi to plant growth. At present, little is known about whether different ginseng cultivars affect the soil rhizosphere microbial community. Results Here, we examined the changes in the microorganismal diversity and composition of the rhizospheres of different ginseng cultivars. We found that fungal communities were more influenced by the cultivars than bacterial communities and revealed differences in the microbial community composition and diversity among the different ginseng cultivars. We found that fungal diversity was negatively correlated with bacterial diversity in CBGL, JYSH and SZSZ; however, TSBT had the lowest bacterial and fungal diversity. We also discovered certain rhizosphere microorganisms that may be associated with pathogenicity and the lifespan of ginseng cultivars, including Bacillus, Alternaria alternata and Cladosporium spp. Conclusions Our results showed that the microbial diversity and community structures under different ginseng cultivars are significantly different and are related to the host cultivar. This result is helpful in providing information that could be used for the breeding of Panax ginseng.

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Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

Biogeosciences Discussions ◽

10.5194/bgd-12-10233-2015 ◽

2015 ◽

Vol 12 (13) ◽

pp. 10233-10269 ◽

Cited By ~ 3

Author(s):

J. Comte ◽

C. Lovejoy ◽

S. Crevecoeur ◽

W. F. Vincent

Keyword(s):

Bacterial Communities ◽

High Throughput Sequencing ◽

Habitat Preferences ◽

Keystone Species ◽

Small World ◽

Rrna Gene ◽

Permafrost Degradation ◽

Bacterial Phyla ◽

Organic Carbon Concentration ◽

Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

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TAXONOMIC STRUCTURE OF PROKARYOTIC COMMUNITIES IN SOILS OF DIFFERENT BIOCLIMATIC ZONES

Dokuchaev Soil Bulletin ◽

10.19047/0136-1694-2018-95-125-153 ◽

2018 ◽

pp. 125-153 ◽

Cited By ~ 2

Author(s):

I. A. Tikhonovich ◽

T. I. Chernov ◽

A. D. Zhelezova ◽

A. K. Tkhakakhova ◽

E. E. Andronov ◽

...

Keyword(s):

High Throughput Sequencing ◽

Profile Analysis ◽

Chestnut Soil ◽

Diversity Indices ◽

Taxonomic Structure ◽

Typical Chernozem ◽

Bacterial Phyla ◽

Dry Steppe ◽

Full Profile ◽

The Difference

Using high-throughput sequencing, we performed a full-profile analysis of the taxonomic structure and diversity of prokaryotic communities of zonal soil series: sod-podzolic, dark gray, typical chernozem, brown soil, meadow-chestnut soil and solonets. Phyla Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia formed up to 95% of prokaryotic communities in all studied soil horizons. Phyla Proteobacteria and Actinobacteria and archaeal phylum Thaumarchaeota dominated in all soils. We revealed the trends of changes in the representation of bacterial phyla in the soils of the zonal range from taiga to dry-steppe: a decrease of Acidobacteria and an increase of Actinobacteria in the upper horizons. The diversity indices of the prokaryotic communities of different genetic horizons of the studied soils were evaluated. In all soils, a decrease in diversity indices with the depth of the horizon was revealed. In all soils, a decrease in diversity indices with depth of the horizon was found, with a rare and slight increase in some lower horizons: structural metamorphic (BM), textural (BT) or accumulative carbonate (BCA) horizons. When examining the prokaryotic communities of soils with different genesis, no determining influence of pH and organic matter contents on the diversity indices was found. Differences in the taxonomic structure and diversity of prokaryotic communities of soils of different bioclimatic zones were presented due to a combination of factors: the difference in chemical and physical properties of soils, as well as in water and temperature conditions.

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Changes in the Density and Composition of Rhizosphere Pathogenic Fusarium and Beneficial Trichoderma Contributing to Reduced Root Rot of Intercropped Soybean

10.21203/rs.3.rs-1067184/v1 ◽

2021 ◽

Author(s):

Xiaoli Chang ◽

Huiting Xu ◽

Li Yan ◽

Dan Zhu ◽

Wei Wang ◽

...

Keyword(s):

Root Rot ◽

Cell Walls ◽

Rhizosphere Soil ◽

Fusarium Species ◽

Inhibitory Effect ◽

Trichoderma Species ◽

Soybean Root ◽

The Difference ◽

Rhizosphere Microbial Community

Abstract BackgroundThe dynamic of soil-borne disease is closely related to the rhizosphere microbial communities. Maize-soybean intercropping can suppress soybean root rot as compared to monoculture. However, it is still unknown whether rhizosphere microbial community participates in the regulation of intercropped soybean root rot.MethodsIn this study, the difference of rhizosphere Fusarium and Trichoderma community was compared between healthy or root-rotted soybean rhizosphere soil from soybean monoculture and maize-soybean intercropping, and the inhibitory effect of potential biocontrol Trichoderma against pathogenic Fusarium were examined.ResultsThe abundance of rhizosphere Fusarium was remarkably different between intercropping and monoculture, while Trichoderma was largely accumulated in healthy rhizosphere soil of intercropping rather than monoculture. Four rhizosphere Fusarium species identified were all pathogenic to soybean but displayed distinct composition and isolation proportion in the corresponding soil types. As the dominant and most aggressive species, F. oxysporum was more frequently isolated in diseased soil of monoculture. Furthermore, of three Trichoderma species identified, T. harzianum dramatically increased in the rhizosphere of intercropping rather than monoculture as compared to T. virens and T. afroharzianum. For in-vitro antagonism test, Trichoderma strains had antagonistic effects on F. oxysporum with the percentage of mycelial inhibition ranging of 50.59%-92.94%, and they displayed good mycoparasitic abilities against F. oxysporum through coiling around and entering into the hyphae, expanding along cell-cell lumen and even dissolving cell walls of target fungus.ConclusionThese results indicate maize-soybean intercropping significantly increase the density and composition proportion of beneficial Trichoderma to antagonist the pathogenic Fusarium species, thus contributing to the suppression of soybean root rot under intercropping.

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Effect ofBacillus velezensis JC-K3 on Endophytic Bacterial and Fungal Diversity in Wheat Under Salt Stress

Frontiers in Microbiology ◽

10.3389/fmicb.2021.802054 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chao Ji ◽

Xiaohui Wang ◽

Xin Song ◽

Qisheng Zhou ◽

Chaohui Li ◽

...

Keyword(s):

Salt Stress ◽

Community Structure ◽

Microbial Community ◽

Microbial Community Structure ◽

Bacterial Communities ◽

Endophytic Bacteria ◽

Rhizosphere Soil ◽

Fungal Communities ◽

Salt Damage ◽

Bacteria And Fungi

Plant growth-promoting bacteria (PGPB) can effectively reduce salt damage in plants. Currently, there are many studies on the effects of PGPB on the microbial community structure of rhizosphere soil under salt stress, but fewer studies on the community structure of endophytic bacteria and fungi. We propose that inoculation of endophytic bacteria into the rhizosphere of plants can significantly affect the microbial community structure of the plant’s above-ground and underground parts, which may be the cause of the plant’s “Induced Systemic Tolerance.” The isolated endophytes were re-inoculated into the rhizosphere under salinity stress. We found that, compared with the control group, inoculation with endophytic Bacillus velezensis JC-K3 not only increased the accumulation of wheat biomass, but also increased the content of soluble sugar and chlorophyll in wheat, and reduced the absorption of Na in wheat shoots and leaves. The abundance of bacterial communities in shoots and leaves increased and the abundance of fungal communities decreased after inoculation with JC-K3. The fungal community richness of wheat rhizosphere soil was significantly increased. The diversity of bacterial communities in shoots and leaves increased, and the richness of fungal communities decreased. JC-K3 strain improved wheat’s biomass accumulation ability, osmotic adjustment ability, and ion selective absorption ability. In addition, JC-K3 significantly altered the diversity and abundance of endophytic and rhizosphere microorganisms in wheat. PGPB can effectively reduce plant salt damage. At present, there are many studies on the effect of PGPB on the microbial community structure in rhizosphere soil under salt stress, but there are few studies on the community structure changes of endophytic bacteria and fungi in plants.

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Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

Biogeosciences ◽

10.5194/bg-13-175-2016 ◽

2016 ◽

Vol 13 (1) ◽

pp. 175-190 ◽

Cited By ~ 31

Author(s):

J. Comte ◽

C. Lovejoy ◽

S. Crevecoeur ◽

W. F. Vincent

Keyword(s):

Bacterial Communities ◽

High Throughput Sequencing ◽

Habitat Preferences ◽

Microbial Consortia ◽

Rrna Gene ◽

Permafrost Degradation ◽

Food Web Structure ◽

Bacterial Phyla ◽

Organic Carbon Concentration ◽

Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north–south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This “small world network” property would render the communities more robust to environmental change but vulnerable to the loss of microbial “keystone species”. These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

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Impact of long-term industrial contamination on the bacterial communities in urban river sediments

10.21203/rs.3.rs-17997/v2 ◽

2020 ◽

Author(s):

lei zhang ◽

Demei Tu ◽

Xingchen Li ◽

Wenxuan Lu ◽

Jing Li

Keyword(s):

Community Structure ◽

Microbial Community ◽

Bacterial Community ◽

Bacterial Communities ◽

Industrial Pollution ◽

River Sediments ◽

Urban River ◽

Bacterial Phyla ◽

Different Types

Abstract Background: The contamination of the aquatic environment of urban rivers with industrial wastewater has affected the abiotic conditions and biological activities of the trophic levels of the ecosystem, particularly sediments. However, most current research about microorganism in urban aquatic environments has focused on indicator bacteria related to feces and organic pollution. Meanwhile, they ignored the interactions among microorganisms. To deeply understand the impact of industrial contamination on microbial community, we study the bacterial community structure and diversity in river sediments under the influence of different types of industrial pollution by Illumina MiSeq high-throughput sequencing technology and conduct a more detailed analysis of microbial community structure through co-occurrence networks.Results: Although the composition of dominant bacterial phyla in different sediment samples was similar, their relative abundance was different. These dominant bacterial phyla showed significant differences in different types of industrial contaminated sediment. In addition, redundancy analysis indicated that the structure of the bacterial community in river sediments was influenced by a variety of environmental factors. TN, TP, TOC and metals (Cu, Zn and Cd) were the most important driving factors that determined the bacterial community in urban river sediments (P <0.01). According to PICRUSt analysis, the bacterial communities in different locations had similar overall functional profiles. It is worth noting that the 15 functional genes related to xenobiotics biodegradation and metabolism were the most abundant in the same location. The non-random assembly patterns of bacterial composition in different types of industrially polluted sediments were determined by a co-occurrence network. Environmental conditions resulting from different industrial pollutants may play an important role in determining their co-occurrence patterns of these bacterial taxa. Among them, the bacterial taxa involved in carbon and nitrogen cycles in module I were relatively abundant, and the bacterial taxa in module II were involved in the repair of metal pollution.Conclusions: Our data indicate that long-term potential interactions between different types of industrial pollution and taxa collectively affect the structure of the bacterial community in urban river sediments.

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Control of Streptomyces alfalfae XY25T Over Clubroot Disease and Its Effect on Rhizosphere Microbial Community in Chinese Cabbage Field Trials

Frontiers in Microbiology ◽

10.3389/fmicb.2021.641556 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yuanliang Hu ◽

Lu Qiu ◽

Zongjie Zhang ◽

Kai Liu ◽

Xian Xia ◽

...

Keyword(s):

Microbial Community ◽

Chinese Cabbage ◽

Field Experiments ◽

Available Phosphorus ◽

Sequencing Analysis ◽

Clubroot Disease ◽

Great Ability ◽

Bacterial Phyla ◽

Significant Difference ◽

Rhizosphere Microbial Community

Clubroot caused by Plasmodiophora brassicae is one of the most destructive diseases in cruciferous crops. Streptomyces alfalfae XY25T, a biological control agent, exhibited great ability to relieve clubroot disease, regulate rhizosphere bacterial and fungal communities in Chinese cabbage, and promote its growth in greenhouse. Therefore, field experiments were carried out to investigate the effects of S. alfalfae XY25T on clubroot and rhizosphere microbial community in Chinese cabbage. Results showed that the control efficiency of clubroot by S. alfalfae XY25T was 69.4%. Applying the agent can alleviate soil acidification; increase the contents of soil organic matter, available nitrogen, available phosphorus, and available potassium; and enhance activities of invertase, urease, catalase, and alkaline phosphatase. During Chinese cabbage growth, bacterial diversity decreased first and then increased, and fungal diversity decreased gradually after inoculation with S. alfalfae XY25T. High-throughput sequencing analysis showed that the main bacterial phyla were Proteobacteria, Bacteroidetes, Acidobacteria, and Planctomycetes, and the major fungal phyla were Ascomycota and Basidiomycota in rhizosphere soil. The dominant bacterial genera were Flavobacterium, Candidatus, Pseudomonas, Stenotrophomonas, Sphingomonas, Flavisolibacter, and Gemmatimonbacteria with no significant difference in abundance, and the major fungal genera were Monographella, Aspergillus, Hypocreales, Chytridiaceae, Fusarium, Pleosporales, Agaricales, Mortierella, and Pleosporales. The significant differences were observed among Pleosporales, Basidiomycota, Colletotrichum, two strains attributed to Agaricales, and another two unidentified fungi by using S. alfalfae XY25T. Moreover, quantitative real-time PCR results indicated that P. brassicae content was significantly decreased after the agent inoculation. In conclusion, S. alfalfae XY25T can affect rhizosphere microbial communities; therefore, applying the agent is an effective approach to reduce the damage caused by clubroot.

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