The Effects of Microbial Inoculants on Bacterial Communities of the Rhizosphere Soil of Maize

The bacterial community of rhizosphere soil maintains soil properties, regulates the microbiome, improves productivity, and sustains agriculture. However, the structure and function of bacterial communities have been interrupted or destroyed by unreasonable agricultural practices, especially the excessive use of chemical fertilizers. Microbial inoculants, regarded as harmless, effective, and environmentally friendly amendments, are receiving more attention. Herein, the effects of three microbial inoculants, inoculant M and two commercial inoculants (A and S), on bacterial communities of maize rhizosphere soil under three nitrogen application rates were compared. Bacterial communities treated with the inoculants were different from those of the non-inoculant control. The OTU (operational taxonomic unit) numbers and alpha diversity indices were decreased by three inoculants, except for the application of inoculant M in CF group. Beta diversity showed the different structures of bacterial communities changed by three inoculants compared with control. Furthermore, key phylotypes analyses exhibited the differences of biomarkers between different treatments visually. Overall, inoculant M had shared and unique abilities of regulating bacterial communities compared with the other two inoculants by increasing potentially beneficial bacteria and decreasing the negative. This work provides a theoretical basis for the application of microbial inoculants in sustainable agriculture.

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A Degeneration Gradient of Poplar Trees Contributes to the Taxonomic, Functional, and Resistome Diversity of Bacterial Communities in Rhizosphere Soils

International Journal of Molecular Sciences ◽

10.3390/ijms22073438 ◽

2021 ◽

Vol 22 (7) ◽

pp. 3438

Author(s):

Juan Liu ◽

Xiangwei He ◽

Jingya Sun ◽

Yuchao Ma

Keyword(s):

Soil Fertility ◽

Microbial Diversity ◽

Resistance Genes ◽

Bacterial Communities ◽

Rhizosphere Soil ◽

Antibiotics Resistance ◽

Plant Growth Promoting Bacteria ◽

Soil Microbial Diversity ◽

Antibiotic Target ◽

And Function

Bacterial communities associated with roots influence the health and nutrition of the host plant. However, the microbiome discrepancy are not well understood under different healthy conditions. Here, we tested the hypothesis that rhizosphere soil microbial diversity and function varies along a degeneration gradient of poplar, with a focus on plant growth promoting bacteria (PGPB) and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG (antibiotics resistance genes) annotation revealed that available potassium (AK) was correlated with microbial diversity and function. We proposed several microbes, Bradyrhizobium, Sphingomonas, Mesorhizobium, Nocardioides, Variovorax, Gemmatimonadetes, Rhizobacter, Pedosphaera, Candidatus Solibacter, Acidobacterium, and Phenylobacterium, as candidates to reflect the soil fertility and the plant health. The highest abundance of multidrug resistance genes and the four mainly microbial resistance mechanisms (antibiotic efflux, antibiotic target protection, antibiotic target alteration, and antibiotic target replacement) in healthy poplar rhizosphere, corroborated the relationship between soil fertility and microbial activity. This result suggested that healthy rhizosphere soil harbored microbes with a higher capacity and had more complex microbial interaction network to promote plant growing and reduce intracellular levels of antibiotics. Our findings suggested a correlation between the plant degeneration gradient and bacterial communities, and provided insight into the role of high-turnover microbial communities as well as potential PGPB as real-time indicators of forestry soil quality, and demonstrated the inner interaction contributed by the bacterial communities.

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Contrasting patterns of bacterial communities in the rearing water and gut of Penaeus vannamei in response to exogenous glucose addition

Marine Life Science & Technology ◽

10.1007/s42995-021-00124-9 ◽

2022 ◽

Author(s):

Lei Huang ◽

Haipeng Guo ◽

Zidan Liu ◽

Chen Chen ◽

Kai Wang ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Communities ◽

Carbon Sources ◽

Operational Taxonomic Unit ◽

Diversity Indices ◽

Response Patterns ◽

Interspecies Interactions ◽

Glucose Addition ◽

Growth And Survival ◽

Α Diversity

AbstractSupplementing exogenous carbon sources is a practical approach to improving shrimp health by manipulating the microbial communities of aquaculture systems. However, little is known about the microbiological processes and mechanisms of these systems. Here, the effects of glucose addition on shrimp growth performance and bacterial communities of the rearing water and the shrimp gut were investigated to address this knowledge gap. The results showed that glucose addition significantly improved the growth and survival of shrimp. Although the α-diversity indices of both bacterioplankton communities and gut microbiota were significantly decreased by adding glucose, both bacterial communities exhibited divergent response patterns to glucose addition. Glucose addition induced a dispersive bacterioplankton community but a more stable gut bacterial community. Bacterial taxa belonging to Ruegeria were significantly enriched by glucose in the guts, especially the operational taxonomic unit 2575 (OTU2575), which showed the highest relative importance to the survival rate and individual weight of shrimp, with the values of 43.8 and 40.6%, respectively. In addition, glucose addition increased the complexity of interspecies interactions within gut bacterial communities and the network nodes from Rhodobacteraceae accounted for higher proportions and linked more with the nodes from other taxa in the glucose addition group than that in control. These findings suggest that glucose addition may provide a more stable gut microbiota for shrimp by increasing the abundance of certain bacterial taxa, such as Ruegeria.

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Microbiome Analysis of Gut Bacterial Communities of Healthy and Diseased Malaysian Mahseer (Tor tambroides)

10.1101/2021.12.08.471852 ◽

2021 ◽

Author(s):

Melinda Mei Lin Lau ◽

Cindy Jia Yung Kho ◽

LEONARD WHYE KIT LIM ◽

Siew Chuiang Sia ◽

Hung Hui Chung ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Communities ◽

Alpha Diversity ◽

Microbiota Composition ◽

Petechial Haemorrhage ◽

Rdna Sequencing ◽

Degrading Bacteria ◽

And Function ◽

Gut Microbial Community ◽

Gut Microbiota Composition

Aims: The gut microbiota is referred to an extra organ and is ciritical in assisting the host in terms of nutrition and immunity. Environmental stressors could alter gut microbial community and cause gut inflammation. This study aimed to investigate and compare the gut microbiota community between healthy and diseased Tor tambroides. Methodology and results: In this study, such gut microbial alterations were explored using NGS-based 16S rDNA sequencing on the Malaysian mahseer (T. tambroides). Three adult healthy and three diseased adult Malaysian mahseers (showing signs of exophthalmia, coelomic distension and petechial haemorrhage) were obtained from LTT Aquaculture Sdn Bhd. Our results revealed significant differences in microbial diversity, composition and function between both populations of T. tambroides. Alpha diversity analysis depicts lower diversity of gut microbiota composition in diseased T. tambroides as compared to the healthy group. In particular, Enterobacteriaceae, Aeromonas, Bacteroides, Vibrio and Pseudomonas were found within gut microbiota of the diseased fishes. In addition, cellulose-degrading bacteria and protease-producing bacteria were identified from the gut of T. tambroides. Conclusion, significance and impact of study: Thus, our findings emphasised on the association between the alteration in gut microbiota composition and infectious abdominal dropsy (IAD) in T. tambroides. This finding is important to provide basic information for further diagnosis, prevention and treatment of intestinal diseases in fish.

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Bacterial community characteristics and enzyme activities in Imperata cylindrica litter as phytoremediation progresses in a copper tailings dam

PeerJ ◽

10.7717/peerj.9612 ◽

2020 ◽

Vol 8 ◽

pp. e9612

Author(s):

Tong Jia ◽

Tingyan Guo ◽

Baofeng Chai

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Chemical Properties ◽

Alpha Diversity ◽

Imperata Cylindrica ◽

Copper Tailings ◽

Α Diversity ◽

Degraded Ecosystems ◽

And Function

This study analyzed Imperata cylindrica litter to determine variation in bacterial community composition and function along with enzyme activity as phytoremediation progresses. We found significant differences in physical and chemical properties of soil and litter in the different sub-dams investigated. The Actinobacteria, Gammaproteobacteria and Alphaproteobacteria were the dominant bacteria found in the litter of the different sub-dams. The alpha diversity (α-diversity) of litter bacterial community increased over as phytoremediation progressed, while total soil carbon and total litter carbon content were positively correlated to bacterial α-diversity. Total litter carbon and total nitrogen were the key factors that influenced bacterial community structure. Heavy metal can influence the degradation of litters by altering the composition of the microbial community. Furthermore, bacterial communities encoded with alpha-amylase (α-amylase) dominated during the initial phytoremediation stage; however, bacterial communities encoded with hemicellulase and peroxidase gradually dominated as phytoremediation progressed. Findings from this study provide a basis for exploring litter decomposition mechanisms in degraded ecosystems, which is critically important to understand the circulation of substances in copper tailings dams.

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Microbial Responses to the Reduction of Chemical Fertilizers in the Rhizosphere Soil of Flue-Cured Tobacco

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.812316 ◽

2022 ◽

Vol 9 ◽

Author(s):

Min-Chong Shen ◽

Yu-Zhen Zhang ◽

Guo-Dong Bo ◽

Bin Yang ◽

Peng Wang ◽

...

Keyword(s):

Bacterial Communities ◽

Agricultural Soil ◽

Rhizosphere Soil ◽

Alpha Diversity ◽

Low Fertility ◽

Control Group ◽

Beneficial Bacteria ◽

Chemical Fertilizers ◽

Agricultural Resources ◽

Microbial Responses

The overuse of chemical fertilizers has resulted in the degradation of the physicochemical properties and negative changes in the microbial profiles of agricultural soil. These changes have disequilibrated the balance in agricultural ecology, which has resulted in overloaded land with low fertility and planting obstacles. To protect the agricultural soil from the effects of unsustainable fertilization strategies, experiments of the reduction of nitrogen fertilization at 10, 20, and 30% were implemented. In this study, the bacterial responses to the reduction of nitrogen fertilizer were investigated. The bacterial communities of the fertilizer-reducing treatments (D10F, D20F, and D30F) were different from those of the control group (CK). The alpha diversity was significantly increased in D20F compared to that of the CK. The analysis of beta diversity revealed variation of the bacterial communities between fertilizer-reducing treatments and CK, when the clusters of D10F, D20F, and D30F were separated. Chemical fertilizers played dominant roles in changing the bacterial community of D20F. Meanwhile, pH, soil organic matter, and six enzymes (soil sucrase, catalase, polyphenol oxidase, urease, acid phosphatase, and nitrite reductase) were responsible for the variation of the bacterial communities in fertilizer-reducing treatments. Moreover, four of the top 20 genera (unidentified JG30-KF-AS9, JG30-KF-CM45, Streptomyces, and Elsterales) were considered as key bacteria, which contributed to the variation of bacterial communities between fertilizer-reducing treatments and CK. These findings provide a theoretical basis for a fertilizer-reducing strategy in sustainable agriculture, and potentially contribute to the utilization of agricultural resources through screening plant beneficial bacteria from native low-fertility soil.

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Resource diversity structures aquatic bacterial communities

10.1101/387803 ◽

2018 ◽

Cited By ~ 1

Author(s):

Mario E. Muscarella ◽

Claudia M. Boot ◽

Corey D. Broeckling ◽

Jay T. Lennon

Keyword(s):

Organic Matter ◽

Bacterial Communities ◽

Alpha Diversity ◽

Structure And Function ◽

Community Diversity ◽

Resource Heterogeneity ◽

Resource Concentration ◽

And Function ◽

Resource Diversity ◽

The Relationship

ABSTRACTMicrobial diversity is strongly affected by the bottom-up effects of resource availability. However, because resource pools often exist as heterogeneous mixtures of distinct molecules, resource heterogeneity may also affect community diversity. To test this hypothesis, we surveyed bacterial communities in lakes that varied in resource concentration. In addition, we characterized resource heterogeneity in these lakes using an ecosystem metabolomics approach. Overall, resource concentration and resource heterogeneity affected bacterial resource-diversity relationships. We found strong relationships between bacterial alpha-diversity (richness and evenness) and resource concentration and richness, but richness and evenness responded in different ways. Likewise, we found associations between the composition of the bacterial community and both resource concentration and composition, but the relationship with resource composition was stronger. Last, in the surveyed communities the presence of resource generalists may have reduced the effect of resource heterogeneity on community composition. These results have implications for understanding the interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.

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Identification of a Phosphorus-Solubilizing Tsukamurella Tyrosinosolvens Strain and its Effect on the Bacterial Diversity of the Rhizosphere Soil of Peanuts Growth-Promoting

10.21203/rs.3.rs-251104/v1 ◽

2021 ◽

Author(s):

Lizhen Han ◽

Hong Zhang

Keyword(s):

Bacterial Communities ◽

Rhizosphere Soil ◽

Ph Value ◽

Alpha Diversity ◽

Significant Negative Correlation ◽

Potassium Nitrate ◽

P Solubilization ◽

Significant Difference ◽

Growth Promoting ◽

Phosphate Solubilizing

Abstract Phosphate Solubilizing Microorganisms widely exist in plant rhizosphere soil, but report about the P solubilization and multiple growth-promoting properties of rare actinomycetes are scarce. In this paper, a phosphate solubilizing Tsukamurella tyrosinosolvens P9 strain was isolated from the rhizosphere soil of tea plants. Phosphorus-dissolving abilities of this strain were different under different carbon and nitrogen sources, the soluble phosphorus content was 442.41 mg/L with glucose and potassium nitrate as nutrient sources. The secretion of various organic acids, such as lactic acid, maleic acid, oxalic acid, etc, was the main mechanism for P solubilization and pH value in culture was very significant negative correlation with soluble P content. In addition, this strain had multiple growth-promoting characteristics with 37.26 μg/mL of IAA and 72.01% of siderophore relative content. Under pot experiments, P9 strain improved obviously the growth of peanut seedlings. The bacterial communities of peanut rhizoshpere soil were assessed after inoculated with P9 strain. It showed that there was no significant difference in alpha-diversity indices between the inoculation and control groups, but the P9 treatment group changed the composition of bacterial communities, which increased the relative abundance of beneficial and functional microbes, which relative abundances of Chitinophagaceae and Beijerinckiaceae at the family level, and of Flavihumibacter , Ramlibacter and Microvirga at the genus level, were all siginificant increased. Specially, Tsukamurella tyrosinosolvens were only detected in the rhizosphere of the inoculated group. This study not only founded growth-promoting properties of T . tyrosinosolvens P9 strain and its possible phosphate solublizing mechanism, but also expected to afford an excellent strain resource in biological fertilizers.

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Diversity and space–time dynamics of the bacterial communities in cotton (Gossypium hirsutum) rhizosphere soil

Canadian Journal of Microbiology ◽

10.1139/cjm-2019-0196 ◽

2020 ◽

Vol 66 (3) ◽

pp. 228-242

Author(s):

YingWu Shi ◽

HongMei Yang ◽

Ming Chu ◽

XinXiang Niu ◽

XiangDong Huo ◽

...

Keyword(s):

Bacterial Communities ◽

Rhizosphere Soil ◽

Operational Taxonomic Unit ◽

Rhizosphere Bacteria ◽

Growth Stages ◽

Time Dynamics ◽

Opposite Trend ◽

Α Diversity ◽

Generation Sequencing ◽

Southern Xinjiang

Rhizosphere bacteria are key determinants of plant health and productivity. In this study, we used PCR-based next-generation sequencing to reveal the diversity and community composition of bacteria in the cotton rhizosphere from samples collected in Xinjiang Province, China. We identified 125 bacterial classes within 49 phyla from these samples. Proteobacteria (33.07% of total sequences), Acidobacteria (19.88%), and Gemmatimonadetes (11.19%) dominated the bacterial community. Marked differences were evident in the α-diversity of rhizosphere bacteria during different cotton plant growth and development stages. The operational taxonomic unit (OTU) numbers were highest in seedling and bud stages and decreased at the flowering and fruit-boll-opening stages. Forty-three OTUs from the Proteobacteria were common to all four periods of cotton development. Proteobacteria were more abundant in the rhizospheres of cotton from southern Xinjiang than from northern Xinjiang, while the opposite trend was observed for Acidobacteria. Gemmatimonadetes frequency was broadly the same in both northern and southern Xinjiang. These results suggest that there is abundant diversity in the microbiota of cotton rhizosphere soil. Proteobacteria and Actinobacteria dominated this microbial niche and bacterial communities in the seedling, bud, flowering, and boll-opening stages appear to be more similar to one another than to communities at the other growth stages.

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Tibetan wild asses (Equus Kiang) were superior to domestic donkeys (Equus Asinus) in terms of the composition and function of gut microbial community

10.21203/rs.2.19346/v1 ◽

2019 ◽

Author(s):

Hongjin Liu ◽

Xinquan Zhao ◽

Shixiao Xu ◽

Liang Zhao ◽

Xueping Han ◽

...

Keyword(s):

Bacterial Communities ◽

Metabolic Pathways ◽

Species Interactions ◽

High Throughput Sequencing ◽

Acid Metabolism ◽

Alpha Diversity ◽

Equus Asinus ◽

Significant Difference ◽

And Function ◽

Gut Microbial Community

Abstract Tibetan wild asses (Equus Kiang) are the only wild species of perissodactyls on the Qinghai-Tibetan Plateau, and appears on the International Union for Conversation of Nature (IUCN) 2012 Red List of threatened species. Therefor, understanding the gut microbita composition and function can provide a theoretical for the situ conservation of wild animals in the future. This study analyzed the intestinal microbiota of wild asses and domestic donkeys by high-throughput sequencing of the 16s rDNA regions. No significant difference in alpha diversity was detected between these two groups. Beta diversity showed that the bacterial community structure of wild asses was acutely different from domestic donkeys. At the phylum level, the two dominant phyla of Bacteroidetes and Firmcutes in wild asses were significantly higher than that in domestic donkeys. At the genus level, Ruminococcaceae_NK4A214, Phascolarctobacterium, Coprostanoligenes_group, Lachnospiraceae_XPB1014_group and Akkermansia in wild asses were significantly higher than domestic donkeys. Moreover, statistical comparisons showed that 40 different metabolic pathways exhibited significant differences. Among them, 29 pathways had richer concentrations in wild asses than domestic donkeys, mainly included amino acid metabolism, carbohydrate metabolism, and energy metabolism. Of note, network analysis showed that wild asses harbored a relatively more complex bacterial network than domestic donkeys, possibly reflecting the specific niche adaption of gut bacterial communities through species interactions. The overall results indicated that wild asses were superior to that of domestic in gut bacteria community composition and function, and wild asses should be more suitable to survive in wild than to be domesticated or captive.

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Seasonal Variation Imparts The Endophytic Bacterial Community Dynamics in Mango Plants and Its Hemiparasites

10.21203/rs.3.rs-641910/v1 ◽

2021 ◽

Author(s):

Rajsekhar Adhikary ◽

Sukhendu Mandal ◽

Vivekananda Mandal

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Community Dynamics ◽

Mangifera Indica ◽

Alpha Diversity ◽

Diversity Indices ◽

Rrna Gene ◽

Flowering Season ◽

Bacterial Community Dynamics ◽

Endophytic Community

Abstract Assessment of bacterial community dynamics helps to estimate the endophytic community structure and ecological behaviour imposed by them. Such community composition is essential to understand the molecular interplay that lies between them and the host plants. The present study aims to explore the endophytic bacterial communities and their dynamics in the pre-flowering and post-flowering seasons in the horticulturally important Mango (Mangifera indica L.) and its hemiparasites Loranthus sp., and Macrosolen sp. through a metagenomic approach using the sequence of V3 region of 16S rRNA gene. Bacillus was found to be the most abundant genera, followed by Acinetobacter, and Corynebacterium, which belong to the phyla Firmicutes, Proteobacteria, and Actinobacteria. It has been found that during the post-flowering season, twigs and leaves of mango have lower endophytic bacterial loads. Furthermore, the alpha-diversity indices of the representative genera were highest in Loranthus sp. during the post-flowering seasons of mango. The ecological, taxonomic, and complex correlation studies unravelled that the hemiparasites act as the potent reservoirs of endophytic community throughout the year, and during favourable conditions, these bacterial communities disseminate to the mango plant.

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