Seasonal changes driving shifts of aquatic rhizosphere microbial community structure and the functional properties

Zhang, Jiawei; Ge, Zuhan; Ma, Zihang; Huang, Danni; Zhang, Jibiao

doi:10.1016/j.jenvman.2022.116124

Cited by 24 publications

(3 citation statements)

References 47 publications

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“…As in water, the abundance for CL500-29 marine group, Acinetobacter and hgcI-clade ( Cyanobacteria ) were significantly higher in comparison with plant groups. Similar results were obtained from static water in ecological floating beds (EFBs), showing that Cyanobacteria and CL500-29 marine group are dominant taxa ( Zhang et al., 2022 ). The thriving of Cyanobacteria indicated a certain degree of eutrophication of the lake water.…”

Section: Discussionsupporting

confidence: 69%

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Fan,

Schwinghamer,

Liu

et al. 2023

Front. Plant Sci.

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IntroductionThe endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).MethodsIn the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes.Results and discussionPlant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.

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Section: Discussionsupporting

confidence: 69%

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Fan,

Schwinghamer,

Liu

et al. 2023

Front. Plant Sci.

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“…Rhodobacter is diverse in bacterial metabolism and can decompose organic matter through photosynthesis (Ren et al 2020). It also has denitrification and nitrogen fixation functions (Zhang et al 2022b). Hydrogenopha is an autotrophic denitrifying bacterium with certain nitrogen fixation function (Lin et al 2018 andSi et al 2020), and its relative abundance in EFB-PS (2.21%) and EFB-S (5.89%) is also higher than that in EFB-P (0.11%).…”

Section: Microbial Community Compositionmentioning

confidence: 99%

Effect of zeolite–sponge iron combined substrate on microbial community in ecological floating bed

Meng,

Cheng,

Ren

et al. 2023

Environ. Res. Commun.

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Substrate has been proven to be a useful way to enhance the purification effect of ecological floating bed (EFB), and it also affected the microbial community. While at cold temperature, there was a lack of research on the effect of substrates on plant growth and microbial communities. In this study, three EFBs, namely plant EFB (EFB-P), substrate EFB (EFB-S) and plant–substrate EFB (EFB-PS), were constructed. The effects of zeolite–sponge iron combined substrate on pollutant removal, plant growth and microbial community in the EFBs were investigated at low temperature (3.1 ~ 11.7℃). Results showed that the removal efficiencies of total nitrogen, total phosphorus and nitrate nitrogen by EFB-PS (60.35%, 95.09% and 64.43%) was significantly better than that of EFB-P (47.71%, 88.59% and 51.65%), but the relative growth of the aboveground biomass of plants (50.41%) was less than that of EFB-P (81.16%). In addition, the microbial biomass in EFB-PS (69.14 mg/(g DW·day)) and EFB-S (68.76 mg/(g DW·day)) was much larger than that in EFB-P (50.69 mg/(g DW·day)). High-throughput sequencing showed that the microbial diversity (Shannon (6.06 ~ 8.33) and Simpson (0.88 ~ 0.97)) and richness (Chao1 (1621.7 ~ 2556.2) and Observed _ species (1437 ~ 2423.3)) of EFB with adding zeolite–sponge iron combined substrate were also higher than those of EFB-P. In addition, the addition of combined substrates changed the microbial community structure, some genera with denitrification and nitrogen fixation functions, including Rhodobacter (36.03 ~ 48.59%), Hydrogenopha (2.21 ~ 5.89 %), were abundantly enriched in the EFB with adding zeolite-sponge iron combined substrate. These results improved the effects of substrate low temperature operation on plant growth and microbial characteristics in EFB, and provide a theoretical basis for strengthening the operation of the low temperature conditions of the EFB.

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“…In addition to emphasising the human microbiota, other animal or environmental microbiota have also been investigated [ 1 – 4 ]. The interaction between microbiomes and the host is an important research direction, as microbiomes play critical roles in nutrient acquisition, immunity, and disease processes that benefit or harm their hosts [ 3 , 5 – 8 ]. Hence, studies on understanding host microbiomes could address many questions associated with the cross-talk between the host and microbial communities, thereby providing many novel findings.…”

Section: Introductionmentioning

confidence: 99%

Bacterial community analysis identifies Klebsiella pneumoniae as a native symbiotic bacterium in the newborn Protobothrops mucrosquamatus

Hussain

Hsu

et al. 2023

BMC Microbiol

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Background The study of the native microbiome of organisms is crucial. The connection between the native microbiome and the host affects the formation of the innate immune system and the organism’s growth. However, the native microbiome of newborn venomous snakes has not been reported. Therefore, we aimed to determine the oral and skin microbiomes of newborn Protobothrops mucrosquamatus. Results We performed 16 S full-length sequencing on 14 samples collected from 7 newborn P. mucrosquamatus individuals, specifically targeting their oral and skin microbiomes. In terms of the oral and skin microbiome, the main species were Klebsiella pneumoniae lineages. According to subspecies/species analysis, the proportion from highest to lowest was K. quasipneumoniae subsp. similipneumoniae, K. pneumoniae subsp. pneumoniae, and K. pneumoniae subsp. rhinoscleromatis. These three bacteria accounted for 62.5% and 85% of the skin and oral activity, respectively. The oral microbiome of newborn P. mucrosquamatus did not comprise common bacteria found in snakebite wounds or oral cultures in adult snakes. Therefore, the source of other microbiomes in the oral cavities of adult snakes may be the environment or prey. Functional Annotation of the Prokaryotic Taxa analysis showed that the skin/oral native microbiome metabolism was related to fermentation and human infection owing to the dominance of K. pneumoniae lineages. The characteristics of K. pneumoniae may impact the development of venom in venomous snakes. Conclusion The results of the native microbiome in the oral cavity and skin of newborn P. mucrosquamatus demonstrated that the habitat environment and prey capture may affect the composition of bacteria in adult snakes. We hypothesized that the native microbiome influences newborn venomous snakes and that K. pneumoniae lineages related to citrate fermentation may play a role in venom growth. However, further verification of this is required.

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Seasonal changes driving shifts of aquatic rhizosphere microbial community structure and the functional properties

Cited by 24 publications

References 47 publications

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Effect of zeolite–sponge iron combined substrate on microbial community in ecological floating bed

Bacterial community analysis identifies Klebsiella pneumoniae as a native symbiotic bacterium in the newborn Protobothrops mucrosquamatus

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