Analysis on Metabolic Functions of Stored Rice Microbial Communities by BIOLOG ECO Microplates

Ge, Zhiwen; Du, Hengjun; Gao, Yulong; Qiu, Wei

doi:10.3389/fmicb.2018.01375

Cited by 78 publications

(37 citation statements)

References 36 publications

(43 reference statements)

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“…BIOLOG ECO Microplates served as an efficient tool to detect microorganism carbon source utilization abilities, which revealed the characteristics of their metabolic functions since different species are able to utilize different carbon sources [33,34]. The microplates consisted of 96 wells divided into three groups, with each group containing a blank well and 31 different sole carbon source (of 6 biochemical categories) wells, providing a triplicated experiment on one plate [35]. Further, a redox dye indicator was contained in each well to reflect the nicotinamide adenine dinucleotide (NADH) production from cell respiration.…”

Section: Methodsmentioning

confidence: 99%

Effects of Nanoplastics on Freshwater Biofilm Microbial Metabolic Functions as Determined by BIOLOG ECO Microplates

Miao

Guo

Liu

et al. 2019

IJERPH

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Nanoplastic (NP) contamination is becoming a pervasive issue as NPs, originating from microplastic particles, pose potentially harmful environmental impacts on aquatic ecosystems. The environmental hazards of NPs on microorganisms have been well documented in recent studies; however, little is known about their ecotoxicity effects on freshwater biofilms, which serve as important primary producers and decomposers and are highly connected with other ecosystem components. We investigated the effects of NPs on the microbial metabolic functions of freshwater biofilms in terms of carbon source utilization ability. Biofilm samples were collected, cultivated in a hydrodynamic flume for six weeks, and then exposed in polystyrene (PS) beads (100 nm in size) with different NP concentrations (1, 5, and 10 mg/L). BIOLOG ECO microplates were used to quantify carbon source utilization characteristics. The data were analyzed using average well-color development (AWCD), functional diversity indices, and principle component analysis (PCA). Results showed that the total carbon metabolic functions (represented by AWCD) remained constant (p > 0.05) with elevated NP concentrations, but some specific carbon sources (e.g., esters) changed in their utilization ability (p < 0.05). The microbial functional diversity (Shannon–Wiener diversity index, Simpson diversity index, and Shannon evenness index) was significantly reduced under 10 mg/L NPs (p < 0.05), indicating an inhibiting effect of NPs on biofilm metabolic diversity. This study examined NP ecotoxicity effects on microbial metabolic activities at the community level, but further studies are required to fully understand the mechanisms driving this change.

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Section: Methodsmentioning

confidence: 99%

Effects of Nanoplastics on Freshwater Biofilm Microbial Metabolic Functions as Determined by BIOLOG ECO Microplates

Miao

Guo

Liu

et al. 2019

IJERPH

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“…By readapting their metabolism, they will be able to continue to proliferate. Biolog Eco plates are primarily used for soil community analysis based on sole-carbon-source utilization (42). In our study, these plates facilitated the identification of the strain with higher metabolic diversity.…”

Section: Discussionmentioning

confidence: 96%

A Framework for the Selection of Plant Growth-Promoting Rhizobacteria Based on Bacterial Competence Mechanisms

Amaya-Gómez

Porcel

Mesa-Garriga

et al. 2020

Appl Environ Microbiol

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ABSTRACT The use of plant growth-promoting rhizobacteria (PGPR) is increasingly meaningful for the development of more environmentally friendly agricultural practices. However, often the PGPR strains selected in the laboratory fail to confer the expected beneficial effects when evaluated in plant experiments. Insufficient rhizosphere colonization is pointed out as one of the causes. With the aim of minimizing this inconsistency, we propose that besides studying plant growth promotion traits (PGP), the screening strategy should include evaluation of the microbial phenotypes required for colonization and persistence. As a model, we carried out this strategy in three Rhizobium sp. strains that showed phosphorus solubilization ability and production of siderophores. All strains displayed colonization phenotypes like surface spreading, resistance to hydrogen peroxide, and formed biofilms. Regarding their ability to persist, biofilm formation was observed to be influenced by pH and the phosphorus nutrient provided in the growth media. Differences in the competence of the strains to use several carbon substrates were also detected. As part of our framework, we compared the phenotypic characteristics of the strains in a quantitative manner. The data analysis was integrated using a multicriteria decision analysis (MCDA). All our results were scored, weighted, and grouped as relevant for PGP, colonization, or persistence. MCDA demonstrated that, when the phenotypes related to PGP and colonization are weighted over those for persistence, strain B02 performs better than the other two Rhizobium sp. strains. The use of our framework could assist the selection of more competent strains to be tested in greenhouse and field trials. IMPORTANCE Numerous plant growth-promoting rhizobacteria (PGPR) have been inoculated into the soil with the aim of improving the supply of nutrients to crop plants and decreasing the requirement of chemical fertilizers. However, sometimes these microbes fail to competitively colonize the plant roots and rhizosphere. Hence, the plant growth promotion effect is not observed. Here, we describe a new screening strategy aiming at the selection of more competent PGPR. We evaluated bacterial phenotypes related to plant growth promotion, colonization, and persistence. Our results demonstrated that despite the fact that our Rhizobium sp. strains successfully solubilized phosphorus and produced siderophores, their abilities to spread over surfaces, resist hydrogen peroxide, and form biofilms varied. Additionally, a multicriteria decision analysis was used to analyze the data that originated from bacterial physiological characterizations. This analysis allowed us to innovatively evaluate each strain as a whole and compare the performances of the strains under hypothetical scenarios of bacterial-trait requirements.

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“…In this study, 31 substrates in the Biolog-ECO plate were assigned to six categories: carbohydrates, carboxylic acids, amino acids, amines, phenolic compounds, and polymers [40]. The varying AWCD value and the final value reflected the utilization ability of microorganisms with respect to a certain carbon source.…”

Section: Shift Of Microbial Clpp With Concentrations Of Zno Npsmentioning

confidence: 99%

Response of the Intertidal Microbial Community Structure and Metabolic Profiles to Zinc Oxide Nanoparticle Exposure

Xinyu

Zhang

et al. 2020

IJERPH

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The toxicity of nanomaterials to microorganisms is related to their dose and environmental factors. The aim of this study was to investigate the shifts in the microbial community structure and metabolic profiles and to evaluate the environmental factors in a laboratory scale intertidal wetland system exposed to zinc oxide nanoparticles (ZnO NPs). Microbial assemblages were determined using 16S rRNA high-throughput sequencing. Community-level physiological profiles were determined using Biolog-ECO technology. Results showed Proteobacteria was the predominant (42.6%–55.8%) phylum across all the sediments, followed by Bacteroidetes (18.9%–29.0%). The genera Azoarcus, Maribacter, and Thauera were most frequently detected. At the studied concentrations (40 mg·L−1, 80 mg·L−1, 120 mg·L−1), ZnO NPs had obvious impacts on the activity of Proteobacteria. Adverse effects were particularly evident in sulfur and nitrogen cycling bacteria such as Sulfitobacter, unidentified_Nitrospiraceae, Thauera, and Azoarcus. The alpha diversity index of microbial community did not reflect stronger biological toxicity in the groups with high NP concentrations (80 mg·L−1, 120 mg·L−1) than the group with low NP concentration (40 mg·L−1). The average well color development (AWCD) values of periodically submersed groups were higher than those of long-term submersed groups. The group with NP concentration (40 mg·L−1) had the lowest AWCD value; those of the groups with high NP concentrations (80 mg·L−1, 120 mg·L−1) were slightly lower than that of the control group. The beta diversity showed that tidal activity shaped the similar microbial community among the periodically submerged groups, as well as the long-term submerged groups. The groups with high DO concentrations had higher diversity of the microbial community, better metabolic ability, and stronger resistance to ZnO NPs than the groups with a low DO concentration.

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Analysis on Metabolic Functions of Stored Rice Microbial Communities by BIOLOG ECO Microplates

Cited by 78 publications

References 36 publications

Effects of Nanoplastics on Freshwater Biofilm Microbial Metabolic Functions as Determined by BIOLOG ECO Microplates

Effects of Nanoplastics on Freshwater Biofilm Microbial Metabolic Functions as Determined by BIOLOG ECO Microplates

A Framework for the Selection of Plant Growth-Promoting Rhizobacteria Based on Bacterial Competence Mechanisms

Response of the Intertidal Microbial Community Structure and Metabolic Profiles to Zinc Oxide Nanoparticle Exposure

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