Field multi-omics analysis reveals a close association between bacterial communities and mineral properties in the soybean rhizosphere

Characterization of soybean chitinase genes induced by rhizobacteria involved in the defense against Fusarium oxysporum

Rhizobacteria are capable of inducing defense responses via the expression of pathogenesis-related proteins (PR-proteins) such as chitinases, and many studies have validated the functions of plant chitinases in defense responses. Soybean (Glycine max) is an economically important crop worldwide, but the functional validation of soybean chitinase in defense responses remains limited. In this study, genome-wide characterization of soybean chitinases was conducted, and the defense contribution of three chitinases (GmChi01, GmChi02, or GmChi16) was validated in Arabidopsis transgenic lines against the soil-borne pathogen Fusarium oxysporum. Compared to the Arabidopsis Col-0 and empty vector controls, the transgenic lines with GmChi02 or GmChi16 exhibited fewer chlorosis symptoms and wilting. While GmChi02 and GmChi16 enhanced defense to F. oxysporum, GmChi02 was the only one significantly induced by Burkholderia ambifaria. The observation indicated that plant chitinases may be induced by different rhizobacteria for defense responses. The survey of 37 soybean chitinase gene expressions in response to six rhizobacteria observed diverse inducibility, where only 10 genes were significantly upregulated by at least one rhizobacterium and 9 genes did not respond to any of the rhizobacteria. Motif analysis on soybean promoters further identified not only consensus but also rhizobacterium-specific transcription factor-binding sites for the inducible chitinase genes. Collectively, these results confirmed the involvement of GmChi02 and GmChi16 in defense enhancement and highlighted the diverse inducibility of 37 soybean chitinases encountering F. oxysporum and six rhizobacteria.

Testing the stress gradient hypothesis in soil bacterial communities associated with vegetation belts in the Andean Atacama Desert

BACKGROUND

Soil microorganisms are in constant interaction with plants, and these interactions shape the composition of soil bacterial communities by modifying their environment. However, little is known about the relationship between microorganisms and native plants present in extreme environments that are not affected by human intervention. Using high-throughput sequencing in combination with random forest and co-occurrence network analyses, we compared soil bacterial communities inhabiting the rhizosphere surrounding soil (RSS) and the corresponding bulk soil (BS) of 21 native plant species organized into three vegetation belts along the altitudinal gradient (2400-4500 m a.s.l.) of the Talabre-Lejía transect (TLT) in the slopes of the Andes in the Atacama Desert. We assessed how each plant community influenced the taxa, potential functions, and ecological interactions of the soil bacterial communities in this extreme natural ecosystem. We tested the ability of the stress gradient hypothesis, which predicts that positive species interactions become increasingly important as stressful conditions increase, to explain the interactions among members of TLT soil microbial communities.

RESULTS

Our comparison of RSS and BS compartments along the TLT provided evidence of plant-specific microbial community composition in the RSS and showed that bacterial communities modify their ecological interactions, in particular, their positive:negative connection ratios in the presence of plant roots at each vegetation belt. We also identified the taxa driving the transition of the BS to the RSS, which appear to be indicators of key host-microbial relationships in the rhizosphere of plants in response to different abiotic conditions. Finally, the potential functions of the bacterial communities also diverge between the BS and the RSS compartments, particularly in the extreme and harshest belts of the TLT.

CONCLUSIONS

In this study, we identified taxa of bacterial communities that establish species-specific relationships with native plants and showed that over a gradient of changing abiotic conditions, these relationships may also be plant community specific. These findings also reveal that the interactions among members of the soil microbial communities do not support the stress gradient hypothesis. However, through the RSS compartment, each plant community appears to moderate the abiotic stress gradient and increase the efficiency of the soil microbial community, suggesting that positive interactions may be context dependent.

Soil bacterial communities of paddy are dependent on root compartment niches but independent of growth stages from Mollisols of Northeast China

Introduction

Deep insights into adhering soil of root zones (rhizosphere and rhizoplane) microbial community could provide a better understanding of the plant-microbe relationship. To better understand the dynamics of these microbial assemblies over the plant life cycle in rhizodeposition along rice roots.

Methods

Here, we investigated bacterial distribution in bulk, rhizosphere, and rhizoplane soils at tillering, heading, and mature stage, from rice (Oryza sativa) fields of the Northeast China.

Results and Discussion

Our results revealed that soil bacterial α-diversity and community composition were significantly affected by root compartment niches but not by temporal change. Compared to rhizoplane soils in the same period, bulk in the heading and rhizosphere in the mature had the largest increase in Shannon's index, with 11.02 and 14.49% increases, respectively. Proteobacteria, Chloroflexi, Bacteroidetes, and Acidobacteria are predominant across all soil samples, bulk soil had more phyla increased across the growing season than that of root related-compartments. Deterministic mechanisms had a stronger impact on the bacterial community in the compartments connected to the roots, with the relative importance of the bulk soil, rhizoplane and rhizosphere at 83, 100, and 56%, respectively. Because of ecological niche drivers, the bacterial networks in bulk soils exhibit more complex networks than rhizosphere and rhizoplane soils, reflected by more nodes, edges, and connections. More module hub and connector were observed in bulk (6) and rhizoplane (5) networks than in rhizosphere (2). We also detected shifts from bulk to rhizoplane soils in some functional guilds of bacteria, which changed from sulfur and nitrogen utilization to more carbon and iron cycling processes. Taken together, our results suggest distinct bacterial network structure and distribution patterns among rhizosphere, rhizoplane, and bulk soils, which could possibly result in potential functional differentiation. And the potential functional differentiation may be influenced by plant root secretions, which still needs to be further explored.

Agroecosystem engineering extended from plant-microbe interactions revealed by multi-omics data

In an agroecosystem, plants and microbes coexist and interact with environmental factors such as climate, soil, and pests. However, agricultural practices that depend on chemical fertilizers, pesticides, and frequent tillage often disrupt the beneficial interactions in the agroecosystem. To reconcile the improvement of crop performance and reduction in environmental impacts in agriculture, we need to understand the functions of the complex interactions and develop an agricultural system that can maximize the potential benefits of the agroecosystem. Therefore, we are developing a system called the agroecosystem engineering system, which aims to optimize the interactions between crops, microbes, and environmental factors, using multi-omics analysis. This review first summarizes the progress and examples of omics approaches, including multi-omics analysis, to reveal complex interactions in the agroecosystem. The latter half of this review discusses the prospects of data analysis approaches in the agroecosystem engineering system, including causal network analysis and predictive modeling.

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling

Microbiota are a major component of agroecosystems. Root microbiota, which inhabit the inside and surface of plant roots, play a significant role in plant growth and health. As next-generation sequencing technology allows the capture of microbial profiles without culturing the microbes, profiling of plant microbiota has become a staple tool in plant science and agriculture. Here, we have increased sample handling efficiency in a two-step PCR amplification protocol for 16S rRNA gene sequencing of plant root microbiota, improving DNA extraction using AMPure XP magnetic beads and PCR purification using exonuclease. These modifications reduce sample handling and capture microbial diversity comparable to that obtained by the manual method. We found a buffer with AMPure XP magnetic beads enabled efficient extraction of microbial DNA directly from plant roots. We also demonstrated that purification using exonuclease before the second PCR step enabled the capture of higher degrees of microbial diversity, thus allowing for the detection of minor bacteria compared with the purification using magnetic beads in this step. In addition, our method generated comparable microbiome profile data in plant roots and soils to that of using common commercially available DNA extraction kits, such as DNeasy PowerSoil Pro Kit and FastDNA SPIN Kit for Soil. Our method offers a simple and high-throughput option for maintaining the quality of plant root microbial community profiling.

The Promises, Challenges, and Opportunities of Omics for Studying the Plant Holobiont

Microorganisms are critical drivers of biological processes that contribute significantly to plant sustainability and productivity. In recent years, emerging research on plant holobiont theory and microbial invasion ecology has radically transformed how we study plant–microbe interactions. Over the last few years, we have witnessed an accelerating pace of advancements and breadth of questions answered using omic technologies. Herein, we discuss how current state-of-the-art genomics, transcriptomics, proteomics, and metabolomics techniques reliably transcend the task of studying plant–microbe interactions while acknowledging existing limitations impeding our understanding of plant holobionts.

Plant growth-promoting rhizobacterial biofertilizers for crop production: The past, present, and future

Recent decades have witnessed increased agricultural production to match the global demand for food fueled by population increase. Conventional agricultural practices are heavily reliant on artificial fertilizers that have numerous human and environmental health effects. Cognizant of this, sustainability researchers and environmentalists have increased their focus on other crop fertilization mechanisms. Biofertilizers are microbial formulations constituted of indigenous plant growth-promoting rhizobacteria (PGPR) that directly or indirectly promote plant growth through the solubilization of soil nutrients, and the production of plant growth-stimulating hormones and iron-sequestering metabolites called siderophores. Biofertilizers have continually been studied, recommended, and even successfully adopted for the production of many crops in the world. These microbial products hold massive potential as sustainable crop production tools, especially in the wake of climate change that is partly fueled by artificial fertilizers. Despite the growing interest in the technology, its full potential has not yet been achieved and utilization still seems to be in infancy. There is a need to shed light on the past, current, and future prospects of biofertilizers to increase their understanding and utility. This review evaluates the history of PGPR biofertilizers, assesses their present utilization, and critically advocates their future in sustainable crop production. It, therefore, updates our understanding of the evolution of PGPR biofertilizers in crop production. Such information can facilitate the evaluation of their potential and ultimately pave the way for increased exploitation.

All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.

What will polyethylene film mulching bring to the root-associated microbial community of Paeonia ostii?

Plastic film mulching can increase crop yield and is widely used in agricultural production, but long-term mulching could adversely affect plant growth. To investigate the related mechanism, we studied the bacterial communities in different root-associated compartments of Paeonia ostii, a perennial oil crop, under polyethylene film mulching for three years by full-length 16S rDNA sequencing technology, and measured the soil physicochemical properties and enzyme activities. We found that enzyme activities and available nutrients in the soil tended to decrease after long-term mulching. Analysis of bacterial community composition revealed that the endosphere may be another potential source of the root-associated microbiome of P. ostii, and the rhizoplane plays a selective gating role in the enrichment processes for P. ostii microbiome assembly. Long-term mulching affected the abundance of dominant bacterial communities in different root-associated compartments and reduced the bacterial richness in the endosphere, but increased bacterial interactions in each compartment, as well as between different compartments. We speculate that this is mainly related to the decrease of litter content and the serious degradation of polyethylene film after long-term mulching, which resulted in microplastics and other harmful substances entering the soil. Our study further explained the reasons for the harm of long-term film mulching on plants to guide the rational use of plastic film. KEY POINTS: •Soil enzyme activities and available nutrients decreased after long-term mulching. •Mulching affected the dominant bacterial abundance in different root-associated compartments. •Mulching increased bacterial interactions among compartments.