Phosphorus Source and Availability Modulate the Rhizosphere Bacterial Community Assembly in Common Bean

Abstract Background Phosphorus (P) availability is the main nutritional factor that limits crops yields in tropical soils due to edaphic processes that lead to P immobilization after mineral fertilization. Considering the potential of the rhizosphere microbiome to transform insoluble P into forms readily available for plant uptake, in this study is proposed that plants with contrasting P uptake efficiency, growing under depleted amounts of P are able to shape distinct bacterial communities in the rhizosphere enriching taxa specialized in P mobilization. Methods We selected two common bean genotypes contrasting in P efficiency uptake and grew them in a soil with a gradient of two different sources of P, triple superphosphate (TSP) or rock phosphate Bayovar (RPB). The rhizosphere bacterial community was assessed by 16S rRNA amplicon sequencing. Data analyses focused in describing the structure of the bacterial communities, identification of OTUs differentially enriched in different treatments, functional metagenomic prediction and cooccurrence network. Results P sources and levels resulted in different rhizosphere bacterial community structure. A high number of differentially enriched OTUs were observed under P depleted conditions in the P-inefficient genotype, mainly belonging to Actinobacteria phylum. The P-inefficient genotype did not show significant differences in the rhizosphere bacterial community assembly growing in different P sources. Predicted metagenome profiles showed the enrichment of bacterial functions involved in P mobilization, in the rhizosphere of the P inefficient genotype cultivated in P depleted conditions. The network analysis revealed that in the rhizosphere of the P-inefficient genotype under P depleted conditions the bacterial community has a higher number of nodes and edges, higher average degree and clustering coeficient when compared to the treatment with optimal P level. Conclusion Our data showed that the uptake of exogenous input resulted in the assembly of a P-competent microbiome in the P-inefficient genotype compared to the efficient one, supporting the hypothesis that the selective pressure for the P uptake engages P-inefficient genotypes in symbiotic relationships with the soil microbiome. These results will pave the way for future experimentation aiming at explore the contribution of this P-competent microbiome to plant growth and development in a range of soil type.

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The capacity of wastewater treatment plants drives bacterial community structure and its assembly

Scientific Reports ◽

10.1038/s41598-019-50952-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Young Kyung Kim ◽

Keunje Yoo ◽

Min Sung Kim ◽

Il Han ◽

Minjoo Lee ◽

...

Keyword(s):

Wastewater Treatment ◽

Community Structure ◽

Bacterial Community ◽

Activated Sludge ◽

Community Assembly ◽

Bacterial Communities ◽

Wastewater Treatment Plants ◽

High Capacity ◽

Operating Conditions ◽

Rrna Gene

Abstract Bacterial communities in wastewater treatment plants (WWTPs) affect plant functionality through their role in the removal of pollutants from wastewater. Bacterial communities vary extensively based on plant operating conditions and influent characteristics. The capacity of WWTPs can also affect the bacterial community via variations in the organic or nutrient composition of the influent. Despite the importance considering capacity, the characteristics that control bacterial community assembly are largely unknown. In this study, we discovered that bacterial communities in WWTPs in Korea and Vietnam, which differ remarkably in capacity, exhibit unique structures and interactions that are governed mainly by the capacity of WWTPs. Bacterial communities were analysed using 16S rRNA gene sequencing and exhibited clear differences between the two regions, with these differences being most pronounced in activated sludge. We found that capacity contributed the most to bacterial interactions and community structure, whereas other factors had less impact. Co-occurrence network analysis showed that microorganisms from high-capacity WWTPs are more interrelated than those from low-capacity WWTPs, which corresponds to the tighter clustering of bacterial communities in Korea. These results will contribute to the understanding of bacterial community assembly in activated sludge processing.

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Long-term nutrient enrichment of an oligotroph-dominated wetland increases bacterial diversity in bulk soils and plant rhizospheres

10.1101/2020.01.08.899781 ◽

2020 ◽

Author(s):

Regina B. Bledsoe ◽

Carol Goodwillie ◽

Ariane L. Peralta

Keyword(s):

Bacterial Community ◽

Bacterial Diversity ◽

Community Composition ◽

Nutrient Enrichment ◽

Bacterial Communities ◽

Nutrient Addition ◽

Soil Microbiome ◽

The Core ◽

Soil Bacterial

ABSTRACTIn nutrient-limited conditions, plants rely on rhizosphere microbial members to facilitate nutrient acquisition, and in return plants provide carbon resources to these root-associated microorganisms. However, atmospheric nutrient deposition can affect plant-microbe relationships by changing soil bacterial composition and by reducing cooperation between microbial taxa and plants. To examine how long-term nutrient addition shapes rhizosphere community composition, we compared traits associated with bacterial (fast growing copiotrophs, slow growing oligotrophs) and plant (C3 forb, C4 grass) communities residing in a nutrient poor wetland ecosystem. Results revealed that oligotrophic taxa dominated soil bacterial communities and that fertilization increased the presence of oligotrophs in bulk and rhizosphere communities. Additionally, bacterial species diversity was greatest in fertilized soils, particularly in bulk soils. Nutrient enrichment (fertilized vs. unfertilized) and plant association (bulk vs. rhizosphere) determined bacterial community composition; bacterial community structure associated with plant functional group (grass vs. forb) was similar within treatments but differed between fertilization treatments. The core forb microbiome consisted of 602 unique taxa, and the core grass microbiome consisted of 372 unique taxa. Forb rhizospheres were enriched in potentially disease suppressive bacterial taxa and grass rhizospheres were enriched in bacterial taxa associated with complex carbon decomposition. Results from this study demonstrate that fertilization serves as a strong environmental filter on the soil microbiome, which leads to distinct rhizosphere communities and can shift plant effects on the rhizosphere microbiome. These taxonomic shifts within plant rhizospheres could have implications for plant health and ecosystem functions associated with carbon and nitrogen cycling.ImportanceOver the last century, humans have substantially altered nitrogen and phosphorus cycling. Use of synthetic fertilizer and burning of fossil fuels and biomass have increased nitrogen and phosphorous deposition, which results in unintended fertilization of historically low-nutrient ecosystems. With increased nutrient availability, plant biodiversity is expected to decline and bacterial communities are anticipated to increase in abundance of copiotrophic taxa. Here, we address how bacterial communities associated with different plant functional types (forb, grass) shift due to long-term nutrient enrichment. Unlike other studies, results revealed an increase in bacterial diversity, particularly, of oligotrophic bacteria in fertilized plots. We observed that nutrient addition strongly determines forb and grass rhizosphere composition, which could indicate different metabolic preferences in the bacterial communities. This study highlights how long-term fertilization of oligotroph-dominated wetlands could alter the metabolism of rhizosphere bacterial communities in unexpected ways.

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The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties

PeerJ ◽

10.7717/peerj.6147 ◽

2019 ◽

Vol 7 ◽

pp. e6147 ◽

Cited By ~ 1

Author(s):

Shu-Hong Wu ◽

Bing-Hong Huang ◽

Jian Gao ◽

Siqi Wang ◽

Pei-Chun Liao

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Chemical Properties ◽

Soil Chemical Properties ◽

Soil Microbiome ◽

Apparent Lack ◽

Soil P ◽

Soil Bacterial Communities ◽

Abundant Otus ◽

Soil Bacterial

Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.

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Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

10.14293/s2199-1006.1.sor-.ppeupdd.v2 ◽

2020 ◽

Author(s):

Zhang tao ◽

Wang Zhongke ◽

Lv Xinhua ◽

Dang Hanli ◽

Zhuang Li

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Community Diversity ◽

Bacterial Community Diversity ◽

Physicochemical Factors ◽

Rhizosphere Bacterial Community ◽

Ferula Sinkiangensis ◽

Rhizosphere Bacterial Communities

Ferula sinkiangensis is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, Ferula sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of Ferula sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and variation trends of Ferula sinkiangensis rhizosphere bacterial community diversity and abundance on a fine spatial scale (Slope position and soil depth) and Found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in Ferula sinkiangensi s rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in Ferula sinkiangensis . In addition, Soil physicochemical factors jointly explained 24.28% of variation in Ferula sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of Ferula sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

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Soil bacterial community triggered by organic matter inputs supports a high-yielding pear production

10.5194/soil-2021-95 ◽

2021 ◽

Author(s):

Li Wang ◽

Xiaomei Ye ◽

Hangwei Hu ◽

Jing Du ◽

Yonglan Xi ◽

...

Keyword(s):

Organic Matter ◽

Soil Organic Matter ◽

Bacterial Community ◽

Bacterial Communities ◽

Structural Equation ◽

Crop Production ◽

Bacterial Community Composition ◽

Soil Microbiome ◽

High Yield ◽

Common Features

Abstract. The roles of microorganisms in enhancing crop production have been demonstrated for a range of cropping systems. Most studies to date, however, have been confined to a limited number of locations, making it difficult to identify general soil biotic and abiotic characteristics underpinning the yield-promotion across various locations. This knowledge gap limits our capacity to harness soil microbiome to improve crop production. Here we used high-throughput amplicon sequencing to investigate the common features of bacterial community composition, ecological networks and physicochemical properties in six yield-invigorating and adjacent yield-debilitating orchards. We found that yield-invigorating soils exhibited higher contents of organic matter than yield-debilitating soils and harboured unique bacterial communities. Greater alpha diversity and higher relative abundances of Planctomycetes and Chloroflexi were observed in yield-debilitating soils. Co-occurrence network analysis revealed that yield-invigorating soils displayed a greater number of meta-modules and a higher proportion of negative links to positive links. Chloroflexi was recognized as a keystone taxon in manipulating the interaction of bacterial communities in yield-invigorating soils. Structural equation modelling showed that soil organic matter, beta diversity of bacterial community, and network connector (Chloroflexi) were key factors supporting high-yield pear production. Altogether, we provide evidence that yield-invigorating soils across a range of locations appear to share common features, including accumulation of soil organic matter, higher microbial diversity, enrichment of key taxa like Chloroflexi, and maintaining a competitive network. These findings have implications for science-based guidance for sustainable food production.

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Variation of rhizosphere bacterial community diversity in the desert ephemeral plant Ferula sinkiangensis across environmental gradients

Scientific Reports ◽

10.1038/s41598-020-75591-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Tao Zhang ◽

Zhongke Wang ◽

Xinhua Lv ◽

Hanli Dang ◽

Li Zhuang

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Community Diversity ◽

Bacterial Community Diversity ◽

Physicochemical Factors ◽

Rhizosphere Bacterial Community ◽

Ferula Sinkiangensis ◽

Rhizosphere Bacterial Communities

Abstract Ferula sinkiangensis (F. sinkiangensis) is a desert short-lived medicinal plant, and its number is rapidly decreasing. Rhizosphere microbial community plays an important role in plant growth and adaptability. However, F. sinkiangensis rhizosphere bacterial communities and the soil physicochemical factors that drive the bacterial community distribution are currently unclear. On this study, based on high-throughput sequencing, we explored the diversity, structure and composition of F. sinkiangensis rhizosphere bacterial communities at different slope positions and soil depths and their correlation with soil physicochemical properties. Our results revealed the heterogeneity and changed trend of F. sinkiangensis rhizosphere bacterial community diversity and abundance on slope position and soil depth and found Actinobacteria (25.5%), Acidobacteria (16.9%), Proteobacteria (16.6%), Gemmatimonadetes (11.5%) and Bacteroidetes (5.8%) were the dominant bacterial phyla in F. sinkiangensis rhizosphere soil. Among all soil physicochemical variables shown in this study, there was a strong positive correlation between phosphorus (AP) and the diversity of rhizosphere bacterial community in F. sinkiangensis. In addition, Soil physicochemical factors jointly explained 24.28% of variation in F. sinkiangensis rhizosphere bacterial community structure. Among them, pH largely explained the variation of F. sinkiangensis rhizosphere bacterial community structure (5.58%), followed by total salt (TS, 5.21%) and phosphorus (TP, 4.90%).

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Selection of r-K strategies by soil bacterial communities in response to grassland degradation

10.22541/au.163825411.15183617/v1 ◽

2021 ◽

Author(s):

Junwei Peng ◽

Hong Liu ◽

Yang Hu ◽

Yang Sun ◽

Qin Liu ◽

...

Keyword(s):

Bacterial Community ◽

Community Assembly ◽

Bacterial Communities ◽

Gene Diversity ◽

Bacterial Community Composition ◽

Nutrient Loss ◽

Grassland Degradation ◽

Response Strategies ◽

Grassland Ecosystems ◽

Soil Bacterial

Numerous studies have investigated bacterial community structure in grassland ecosystems and bacterial community responses to human management at various spatial and temporal scales; however, research on soil bacterial community assembly dynamics in the course of grassland degradation is limited. Here, the authors investigate the response and assembly processes of bacterial communities adopted in two grasslands with different degrees of degradation. Stochastic processes dominated bacterial community assembly processes in response to grassland degradation, with the bacterial diversity decreasing; however, functional gene diversity increased. Furthermore, different phyla exhibited distinct response strategies: Proteobacteria and Bacteroidetes, as r-strategists, exhibited positive responses, with increases in diversity, abundance, and niche width with an increase in grassland degradation, enhancing biodiversity and productivity; other phyla (mainly Acidobacteria) exhibited greater phylogenetic dispersion and functional redundancy, and less niche overlap, highlighting the role of K-strategy in improving community resource-use efficiency in response to resource loss in degraded grasslands. The transition from K- to r- strategy in bacterial communities following grassland degradation could help communities adapt to environmental disturbance in the form of nutrient loss. The results of the present study enhance our understanding of how nutrient loss in natural grassland ecosystems leads to shifts in bacterial community composition and assembly processes mediated by different response strategies of different phyla.

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The possible use of scarce soluble materials as a source of phosphorus in Vicia faba L. grown in calcareous soils

Acta agriculturae Slovenica ◽

10.14720/aas.2021.117.3.1874 ◽

2021 ◽

Vol 117 (3) ◽

pp. 1

Author(s):

Abd-Elmonem Mohamed ELGALA ◽

Shaimaa Hassan ABD-ELRAHMAN

Keyword(s):

Citric Acid ◽

Plant Growth ◽

Vicia Faba ◽

Rock Phosphate ◽

Calcareous Soils ◽

P Uptake ◽

P Availability ◽

High Concentrations ◽

Different Sources ◽

P Sources

Phosphorus (P) is affected by many factors that minimize its solubility especially in calcareous soils. The aim of this work was to conduct laboratory and greenhouse experiments to study the effect of using P solubilizing substances, i.e., compost, humic acid (HA), citric acid and ethylene di-amine tetra acetic acid (EDTA), and rhizobacteria, Bacillus megaterium var. phosphaticum on solubilizing P from different sources, ordinary superphosphate (OSP), rock phosphate (RP) and basic slag (BS). The effect of these treatments on the P- availability in El-Nubaria calcareous soil and P- uptake by faba bean (Vicia faba ‘Giza 843’) were studied. Obtained results showed that the solubility of P sources differs in their ability to release soluble P in the following order: OSP > RP > BS. The following descending order was appeared of available P in soil with addition of solubilizing agents: citric acid > EDTA > HA > compost for these sources of P, for both experiments. Regarding the interaction between solubilizing agents, the treatments of HA combined with EDTA or citric acid were superior in giving high concentrations in soil, and vigor plant growth. In addition, the solubility of P increased by about 5-6 times for all sources in the presence of P- dissolving bacteria. It seemed that the presence of appreciable amounts of Mg, S, Fe, Mn, B and other elements in BS played a role in enhancing plant growth and increasing yield, especially in the presence of added bacteria. BS could be used in calcareous soils and for soils characterized by low nutrient supply as sandy.

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Effects of different vegetable rotations on the rhizosphere bacterial community and tomato growth in a continuous tomato cropping substrate

PLoS ONE ◽

10.1371/journal.pone.0257432 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257432

Author(s):

Li Jin ◽

Jian Lyu ◽

Ning Jin ◽

Jianming Xie ◽

Yue Wu ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Crop Rotation ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Total N ◽

Rhizosphere Bacterial Community ◽

Healthy Growth ◽

Dominant Bacteria

In this study, High throughput sequencing was used to analyze the effects of different vegetable rotations on the rhizosphere bacterial diversity and community structure in a substrate that was used for continuous tomato cropping (CK). The vegetable rotations tested were cabbage/tomato (B), kidney bean/tomato (D), and celery/tomato (Q). The results revealed that the substrate bacterial diversity and richness of each crop rotation were higher than those of CK. The highest bacterial diversity was found in the B substrate, followed by the Q and D substrates. Further comparison showed that the rhizosphere bacterial community structure of Q substrate was significantly different to that of CK. Compared with the CK, the Q substrate had a significantly higher relative abundance of several dominant microflora, such as Acidobacteria, Chloroflexi, and Firmicutes. Additionally, the Q rotation significantly increased the abundance of beneficial bacteria, such as Actinobacteria_unclassified and Anaerolineaceae_unclassified. A redundancy analysis showed that Most dominant bacteria correlated positively with the substrate pH, total N, and alkali-hydrolyzable N but negatively with the available P, available K, total P, total K, and organic matter contents and substrate EC. The substrates after crop rotation improved the growth and physiological condition of the subsequent tomato plants, among which those from the Q rotation performed the best. Therefore, celery rotation not only increased the richness and diversity of bacterial communities in the substrate but also significantly increased the richness of the beneficial bacterial communities, allowing better maintenance of the substrate microenvironment for the healthy growth of crops.

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