scholarly journals Temporal Variability in the Rhizosphere Bacterial and Fungal Community Structure in the Melon Crop Grown in a Closed Hydroponic System

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 719
Author(s):  
Yu-Pin Lin ◽  
Chiao-Ming Lin ◽  
Hussnain Mukhtar ◽  
Hsiao-Feng Lo ◽  
Min-Chun Ko ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Fungal Community ◽  
Temporal Variability ◽  
Bacterial Community Structure ◽  
Fruit Weight ◽  
Growth Stages ◽  
Sequencing Analysis ◽  
Fungal Community Structure

Microbes can establish a pathogenetic or symbiotic relationship with plants in soil and aquatic ecosystems. Although change in bacterial and fungal community in soil and their interaction with plants have been widely studied, little is known about their community structure in hydroponic systems across plant growth stages under different nutrient treatments. This study used next-generation sequencing analysis to assess the temporal changes in melon rhizosphere bacterial and fungal community structure across six different nutrient treatments. We found significant changes in the microbial community composition (especially for bacteria) between growth stages (R = 0.25–0.63, p < 0.01) than nutrient treatments. Proteobacteria dominated the bacterial community at the phylum level across melon growth stages (59.8% ± 16.1%). The genera Chryseobacterium, Pseudomonas, and Massilia dominated the rhizosphere in the flowering and pollination stage, while Brevibacillius showed the highest relative abundance in the harvesting stage. However, the rhizosphere was dominated by uncultured fungal taxa, likely due to the application of fungicides (Ridomil MZ). Further, linear regression analysis revealed a weak influence of bacterial community structure on melon yield and quality, while fruit weight and quality moderately responded to Mg and K deficiency. Nevertheless, the relative abundance of bacterial genus Chryseobacterium in the vegetative stage showed a strong correlation with fruit weight (R2 = 0.75, p < 0.05), while genera Brevibacillus, Lysobacter, and Bosea in late growth stages strongly correlated with fruit sweetness. Overall, temporal variability in the microbial (especially bacterial) community structure exceeds the variability between nutrient treatments for the given range of nutrient gradient while having little influence on melon yield.

scholarly journals Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

2021 ◽  
Author(s):  
Soo-In Sohn ◽  
Jae-Hyung Ahn ◽  
Subramani Pandian ◽  
Young-Ju Oh ◽  
Eun-Kyoung Shin ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Root Nodules ◽  
Growth Stages ◽  
Sequencing Analysis ◽  
Biolog Ecoplate ◽  
Metabolic Capability ◽  
Increasing Trend

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max L.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

scholarly journals Dynamics of Bacterial Community Structure in the Rhizosphere and Root Nodule of Soybean: Impacts of Growth Stages and Varieties

2021 ◽  
Vol 22 (11) ◽  
pp. 5577
Author(s):  
Soo-In Sohn ◽  
Jae-Hyung Ahn ◽  
Subramani Pandian ◽  
Young-Ju Oh ◽  
Eun-Kyoung Shin ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
High Throughput Sequencing ◽  
Root Nodules ◽  
Growth Stages ◽  
Sequencing Analysis ◽  
Biolog Ecoplate ◽  
Metabolic Capability ◽  
Increasing Trend

Bacterial communities in rhizosphere and root nodules have significant contributions to the growth and productivity of the soybean (Glycine max (L.) Merr.). In this report, we analyzed the physiological properties and dynamics of bacterial community structure in rhizosphere and root nodules at different growth stages using BioLog EcoPlate and high-throughput sequencing technology, respectively. The BioLog assay found that the metabolic capability of rhizosphere is in increasing trend in the growth of soybeans as compared to the bulk soil. As a result of the Illumina sequencing analysis, the microbial community structure of rhizosphere and root nodules was found to be influenced by the variety and growth stage of the soybean. At the phylum level, Actinobacteria were the most abundant in rhizosphere at all growth stages, followed by Alphaproteobacteria and Acidobacteria, and the phylum Bacteroidetes showed the greatest change. But, in the root nodules Alphaproteobacteria were dominant. The results of the OTU analysis exhibited the dominance of Bradyrhizobium during the entire stage of growth, but the ratio of non-rhizobial bacteria showed an increasing trend as the soybean growth progressed. These findings revealed that bacterial community in the rhizosphere and root nodules changed according to both the variety and growth stages of soybean in the field.

Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India

Microbiology ◽  
2017 ◽  
Vol 86 (1) ◽  
pp. 136-142 ◽  
Author(s):  
A. Sharma ◽  
D. Paul ◽  
D. Dhotre ◽  
K. Jani ◽  
A. Pandey ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Deep Sequencing ◽  
Bacterial Community Structure ◽  
Hot Spring ◽  
Sequencing Analysis ◽  
Deep Sequencing Analysis

Temporal variability of airborne bacterial community structure in an urban area

2006 ◽  
Vol 40 (40) ◽  
pp. 8074-8080 ◽  
Author(s):  
Pierre A. Maron ◽  
Christophe Mougel ◽  
David P. H. Lejon ◽  
Esmeralda Carvalho ◽  
Karine Bizet ◽  
...  
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Urban Area ◽  
Temporal Variability ◽  
Bacterial Community Structure

scholarly journals Distribution of antibiotic-resistant bacteria in aerobic composting of swine manure with different antibiotics

2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Tingting Song ◽  
Hongna Li ◽  
Binxu Li ◽  
Jiaxun Yang ◽  
Muhammad Fahad Sardar ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Community Structure ◽  
Bacterial Community ◽  
Relative Abundance ◽  
Bacterial Community Structure ◽  
Swine Manure ◽  
Resistant Bacteria ◽  
Absolute Abundance ◽  
Antibiotic Resistant Bacteria ◽  
Antibiotic Resistant

Abstract Background Livestock manure is an important reservoir of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs). The bacterial community structure and diversity are usually studied using high-throughput sequencing that cannot provide direct evidence for ARB changes. Thus, little is known about the distribution of ARB, especially in the presence of different antibiotics in composting process. In this study, the fate of ARB was investigated in aerobic composting of swine manure, using chlortetracycline, sulfamethoxazole, lincomycin, and ciprofloxacin as typical antibiotics. The abundance and species of ARB were analyzed systematically to evaluate their ecological risk at different stages of composting. Results The absolute abundance of total ARB decreased, while the relative abundance increased on day 2. The relative abundance of lincomycin-resistant bacteria was higher than other ARBs during the whole composting process. The absolute abundance of four ARBs was 9.42 × 106–2.51 × 102 CFU/g (lincomycin- > chlortetracycline- > sulfamethoxazole- > ciprofloxacin- > multiple antibiotic-resistant bacteria), and they were not completely inactivated at the end of composting. Antibiotics led to a partial proliferation of ARBs including Corynebacterium, Sporosarcina, Solibacillus, and Acinetobacter. Especially, Corynebacterium, a pathogenic genus, was observed in chlortetracycline and lincomycin treatments. Conclusion Among the antibiotics studied, lincomycin showed the highest ecological risk, due to it expanded the range of lincomycin-resistant bacteria at the phyla level (Firmicutes, Actinobacteria, and Proteobacteria). The principal co-ordinates analysis indicated that the bacterial community structure was primarily associated with the composting stages rather than antibiotic types. Possible potential hosts and the related to the decrease of ARGs abundance were indicated based on the network analysis. The decrease of culturable Proteobacteria and the increase of culturable Firmicutes (Solibacillus, Bacillus) partially explained the high degradation rate of various ARGs with the progress of composting in this study. These results provided important information for the control of antibiotic resistance in composting.

scholarly journals Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Marie-Thérèse Mofini ◽  
Abdala G. Diedhiou ◽  
Marie Simonin ◽  
Donald Tchouomo Dondjou ◽  
Sarah Pignoly ◽  
...  
Keyword(s):  
Community Structure ◽  
Pearl Millet ◽  
Relative Abundance ◽  
Fungal Community ◽  
Management Practices ◽  
Pennisetum Glaucum ◽  
Fungal Communities ◽  
Fungal Community Structure ◽  
The Core ◽  
Factors Influencing

AbstractFungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.

scholarly journals Effects of ultraviolet radiation on the community structure and metabolic pathways of A2O process at Plateau environment

2021 ◽  
Author(s):  
Zong Yongchen ◽  
He Qiang ◽  
Guo Mingzhe ◽  
You Junhao ◽  
Zhang Dongyan
Keyword(s):  
Community Structure ◽  
Water Treatment ◽  
Bacterial Community ◽  
Ultraviolet Radiation ◽  
Relative Abundance ◽  
Ultraviolet Irradiation ◽  
Bacterial Communities ◽  
Metabolic Pathways ◽  
Bacterial Community Structure ◽  
Key Species

Abstract Water treatment ecosystem provides important habitats for various bacterial communities. However, the response mechanism of this ecosystem under ultraviolet rays is not yet clear. In the study, 16S rRNA gene sequencing is used to study the bacterial community structure and metabolic pathways under 5 samples of ultraviolet irradiation times. In general, the bacterial communities of the five samples are different, which indicates that the ultraviolet radiation time has an impact on the bacterial community structure. Analysis of driving factors shows that UV, COD, pH, TN and NH3-N have an impact on the relative abundance of key species. Key species under ultraviolet irradiation are Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Chloroflexi, and Chlamydiae, accounting for 96.69%ཞ98.30%, and ultraviolet irradiation has a significant inhibitory effect on the relative abundance. As the dominant bacterial phyla in Plateau environment, Chlamydiae is discovered for the first time. The network co-occurrence diagrams constructed under different ultraviolet radiation show that each sample is composed of three independent network diagrams. There are 6 common dominant phyla and 33 common dominant bacterial genera in each sample, which reveals that the structure of the ecosystem is composed of more similar microorganisms, rather than random phenomena. It also reflects the competitive relationship between species and the adaptability of bacteria to the environment. Through the analysis of metabolic pathways, it is found that the dominant metabolic pathways in high altitude habitats have certain changes under ultraviolet radiation. Further analysis of carbon, nitrogen and phosphorus metabolic pathways shows that the relative abundance of related metabolic pathways has a certain change, but the difference in metabolic maps is small, that is, the effect of ultraviolet radiation is mainly reflected in the relative abundance of metabolic pathways. These findings indicate that ultraviolet radiation in Plateau environment as an important influencing factor has an impact on microbial structure and metabolic pathways. This research provides an important theoretical basis for further understanding of water treatment ecosystem in Plateau environment, and also provides a new perspective for the development of water treatment ecosystem.

scholarly journals Long-term effects of straw and straw-derived biochar on soil aggregation and fungal community in a rice–wheat rotation system

PeerJ ◽  
2019 ◽  
Vol 6 ◽  
pp. e6171 ◽  
Author(s):  
Naling Bai ◽  
Hanlin Zhang ◽  
Shuangxi Li ◽  
Xianqing Zheng ◽  
Juanqin Zhang ◽  
...  
Keyword(s):  
Community Structure ◽  
Fungal Community ◽  
Soil Samples ◽  
Soil Aggregation ◽  
Inorganic Fertilizer ◽  
Sequencing Analysis ◽  
Fungal Community Structure ◽  
Rotation System ◽  
Straw Return

Background Soil aggregation is fundamental for soil functioning and agricultural productivity. Aggregate formation depends on microbial activity influencing the production of exudates and hyphae, which in turn act as binding materials. Fungi are also important for improving soil quality and promoting plant growth in a symbiotic manner. There is a scarcity of findings comparing the long-term impacts of different yearly double-crop straw return modes (e.g., straw return to the field and straw-derived biochar return to the field) on soil aggregation and fungal community structure in rice–wheat rotation systems. Methods The effects of 6-year continuous straw and straw-derived biochar amendment on soil physicochemical properties and the fungal community were evaluated in an intensively managed crop rotation system (rice–wheat). Soil samples of different aggregates (macroaggregates, microaggregates, and silt clay) from four different fertilization regimes (control, CK; traditional inorganic fertilization, CF; straw returned to field, CS; straw-derived biochar addition, CB) were obtained, and Illumina MiSeq sequencing analysis of the fungal internal transcribed spacer gene was performed. Results Compared to CF, CS and CB enhanced soil organic carbon, total nitrogen, and aggregation in 0–20 and 20–40 cm soil, with CB exhibiting a stronger effect. Additionally, agrowaste addition increased the mean weight diameter and the geometric diameter and decreased the fractal dimension (p < 0.05). Principal coordinates analysis indicated that fertilization management affected fungal community structure and aggregation distribution. In addition, CS increased fungal community richness and diversity, compared to CK, CB decreased these aspects. Ascomycota, unclassified_k_Fungi, and Basidiomycota were the dominant phyla in all soil samples. At the genus level, CB clearly increased fungi decomposing biosolids (Articulospora in macroaggregates in 0–20 cm soil and Neurospora in macroaggregates in 20–40 cm soil); decreased pathogenic fungi (Monographella in macroaggregates and Gibberella in microaggregates in 0–20 cm soil) and CO2-emission-related fungi (Pyrenochaetopsis in microaggregates and silt clay in 0–40 cm soil) (p < 0.05). Straw and biochar with inorganic fertilizer counteracted some of the adverse effects of the inorganic fertilizer with biochar showing better effects than straw.

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