Mechanisms Underlying the Rhizosphere-To-Rhizoplane Enrichment of Cellvibrio Unveiled by Genome-Centric Metagenomics and Metatranscriptomics

Assessment of temperature dynamics during methane oxidation in a pilot scale compost biofilter

Biological methane oxidation can sustain high temperatures in organic matrices, such as landfill covers and compost biofilters. This study investigates the temperature dynamics, methane removal efficiency, and microbial community responses in a pilot scale compost biofilter under three methane concentrations (2, 4, and 8 % v v-1 in air) with a 23-minute empty bed residence time. Complete methane removal was achieved at 2 %, with compost bed temperatures reaching 51 °C. At 4 % and 8 %, temperatures exceeded 60 °C, reducing methane removal efficiency to 97 % and 75 %, respectively, with maximum removal rates of 75 g m-3h-1. Thermotolerant Methylocaldum dominated at temperatures above 50 °C. Elevated temperatures shifted microbial metabolism from anabolism toward catabolism, likely due to thermal stress, as indicated by outlet gas profiles. These findings highlight the importance of optimizing operating conditions, such as moisture control and heat extraction, to balance thermal performance and microbial activity for effective methane biofiltration.

Role of horizontal gene transfer and cooperation in rhizosphere microbiome assembly

Microbes employ a variety of mechanisms, encompassing chemical signaling (e.g., quorum-sensing molecules) and genetic processes like horizontal gene transfer (HGT), to engage in interactions. HGT, in particular, holds a pivotal role as it facilitates the generation of metabolic diversity, thus directly or indirectly influencing microorganisms' interactions and functioning within their habitat. In this study, we investigate the correlations between enhanced metabolic diversity through HGT and cooperative behavior in the rhizosphere. Despite the potential drawbacks of cooperative behavior, which renders it susceptible to exploitation by cheaters based on evolutionary theory, HGT emerges as a mitigating factor. It serves as a valuable and adaptive tool for survival in competitive environments, notably the rhizosphere. By initiating a comprehensive discussion on these processes combined, we anticipate achieving a profound understanding of the rhizosphere microbiome, ultimately enhancing soil microbiology management and the exploitation of this ecological niche.

Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity

Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.

Synergistic biocontrol of Bacillus subtilis and Pseudomonas fluorescens against early blight disease in tomato

Early blight of tomato caused by Alternaria solani results in significant crop losses. In this study, Bacillus subtilis J3 and Pseudomonas fluorescens J8 were co-cultured as a synthetic microbial community (BCA) for synergistic biocontrol of A. solani, and the inhibition mechanism was investigated. BCA presented an inhibition ration against A. solani at 94.91%, which lowered the disease incidence by 38.26-42.87%; reduced peroxidase, catalase, superoxide dismutase activity of tomatoes by 73.11-90.22%; and promoted the biomass by 66.91-489.21%. With BCA protection, the relative expression of tomato resistance genes (including gPAL2, SWRKY, PR-10, and CHI) in roots and leaves was 12.83-90.70% lower than without protection. BCA also significantly altered the rhizosphere and phyllosphere microbial community. The abundance of potentially beneficial bacteria, including Bacillus, Pseudomonas, Arthrobacter, Lysobacter, and Rhizobium, elevated by 6.58-192.77%. They were negatively correlated with resistance gene expression, indicating their vital involvement in disease control. These results provided essential information on the synergistic biocontrol mechanism of bacteria against pathogens, which could contribute to developing novel biocontrol strategies. KEY POINTS: • Bacillus and Pseudomonas present a synergistic biocontrol effect against A. solani. • Biocontrol prevents pathogen damage and improves tomato growth and systemic resistance. • Beneficial bacteria thrive in the rhizosphere is the key to microbial regulation.

Comparison of the colonization ability of Burkholderia strain B23 in the citrus rhizoplane and rhizosphere and assessment of the underlying mechanisms using full-length 16S rDNA amplicon and metatranscriptomic analyses

The characterization of bacterial strains with efficient root colonization ability and the mechanisms responsible for their efficient colonization is critical for the identification and application of beneficial bacteria. In this study, we found that Burkholderia strain B23 exhibited a strong niche differentiation between the rhizosphere and rhizoplane (a niche with more abundant easy-to-use nutrients but stronger selective pressures compared with the tightly adjacent rhizosphere) when inoculated into the field-grown citrus trees. Full-length 16S rDNA amplicon analysis demonstrated that the relative abundance of B23 in the rhizoplane microbiome at 3, 5, and 9 days post-inoculation (dpi) was always higher than that at 1 dpi, whereas its relative abundance in the rhizosphere microbiome was decreased continuously, as demonstrated by a 3.18-fold decrease at 9 dpi compared to 1 dpi. Time-series comparative expression profiling of B23 between the rhizoplane and rhizosphere was performed at representative time points (1, 3, and 9 dpi) through metatranscriptomic analysis, and the results demonstrated that multiple genes involved in the uptake and utilization of easy-to-use carbohydrates and amino acids and those involved in metabolism, energy production, replication, and translation were upregulated in the rhizoplane compared with the rhizosphere at 1 dpi and 3 dpi. Several genes involved in resistance to plant- and microbial competitor-derived stresses exhibited higher expression activities in the rhizoplane compared with the rhizosphere. Furthermore, gene loci responsible for the biosynthesis of the key antifungal and antibacterial metabolites occidiofungin and ornibactin were induced, and their expression levels remained relatively stable from 3 dpi to 9 dpi in the rhizoplane but not in the rhizosphere. Collectively, our findings provide novel lights into the mechanisms underlying the root colonization of the inoculated bacterial strains and serve as a basis for the identification of strains with efficient colonization ability, thus contributing to the development of beneficial bacteria applications.

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.

High Prevalence and Varied Distribution of Antibiotic-Resistant Bacteria in the Rhizosphere and Rhizoplane of Citrus medica

The plant-associated bacteria, including that in the rhizosphere and rhizoplane, play important roles in human exposure to antibiotic-resistant bacteria (ARB). The rhizosphere and rhizoplane represent two distinct environments with different selective pressures for bacterial colonization. However, whether the difference in characteristics between the rhizosphere and rhizoplane can affect the abundance and antibiotic resistance profiles of ARB colonizing, the two environments remain largely unknown. In this study, we obtained 174 bacterial isolates from the rhizosphere (113 isolates) and rhizoplane (61 isolates) of Citrus medica trees grown in a park, where humans could easily and frequently contact the trees. A very high proportion of isolates exhibited resistance to several clinically important antibiotics, including β-lactam class antibiotics and polymyxin, with several known antibiotic-resistant opportunistic pathogens, such as Micrococcus luteus, being identified. The prevalence of ARB in the rhizoplane was higher than that in the rhizosphere. While the prevalence of polymyxin-resistant isolates was higher in the rhizoplane, the prevalence of amphenicol-resistant isolates was significantly higher in the rhizosphere. In summary, our findings suggest that the rhizosphere and rhizoplane are important media for the spread of ARB, and the different characteristics between the two environments can affect the distribution of ARB.

Spatiotemporal Heterogeneity and Intragenus Variability in Rhizobacterial Associations with Brassica rapa Growth

Microbial communities in the rhizosphere are distinct from those in soils and are influenced by stochastic and deterministic processes during plant development. These communities contain bacteria capable of promoting growth in host plants through various strategies. While some interactions are characterized in mechanistic detail using model systems, others can be inferred from culture-independent methods, such as 16S amplicon sequencing, using machine learning methods that account for this compositional data type. To characterize assembly processes and identify community members associated with plant growth amid the spatiotemporal variability of the rhizosphere, we grew Brassica rapa in a greenhouse time series with amended and reduced microbial treatments. Inoculation with a native soil community increased plant leaf area throughout the time series by up to 28%. Despite identifying spatially and temporally variable amplicon sequence variants (ASVs) in both treatments, inoculated communities were more highly connected and assembled more deterministically overall. Using a generalized linear modeling approach controlling for spatial variability, we identified 43 unique ASVs that were positively or negatively associated with leaf area, biomass, or growth rates across treatments and time stages. ASVs of the genus Flavobacterium dominated rhizosphere communities and showed some of the strongest positive and negative correlations with plant growth. Members of this genus, and growth-associated ASVs more broadly, exhibited variable connectivity in networks independent of growth association (positive or negative). These findings suggest host-rhizobacterial interactions vary temporally at narrow taxonomic scales and present a framework for identifying rhizobacteria that may work independently or in concert to improve agricultural yields.

IMPORTANCE The rhizosphere, the zone of soil surrounding plant roots, is a hot spot for microbial activity, hosting bacteria capable of promoting plant growth in ways like increasing nutrient availability or fighting plant pathogens. This microbial system is highly diverse and most bacteria are unculturable, so to identify specific bacteria associated with plant growth, we used culture-independent community DNA sequencing combined with machine learning techniques. We identified 43 specific bacterial sequences associated with the growth of the plant Brassica rapa in different soil microbial treatments and at different stages of plant development. Most associations between bacterial abundances and plant growth were positive, although similar bacterial groups sometimes had different effects on growth. Why this happens will require more research, but overall, this study provides a way to identify native bacteria from plant roots that might be isolated and applied to boost agricultural yields.

Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations

Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.

Recent advances in the bioprospection and applications of chitinolytic bacteria for valorization of waste chitin

One of the most abundant natural polymers on earth, chitin is a fibrous and structural polysaccharide, composed of N-acetyl-D-glucosamine. The biopolymer is the major structural constituent of fungi, arthropods, mollusks, nematodes, and some algae. The biodegradation of chitin is largely manifested by chitinolytic enzyme secreting organisms including bacteria, insects, and plants. Among them, bacterial chitinases represent the most promising, inexpensive, and sustainable source of proteins that can be employed for industrial-scale applications. To this end, the presented review comes at a timely moment to highlight the major sources of chitinolytic bacteria. It also discusses the potential pros and cons of prospecting bacterial chitinases that can be easily manipulated through genetic engineering. Additionally, we have elaborated the recent applications of the chitin thereby branding chitinases as potential candidates for biorefinery and biomedical research for eco-friendly and sustainable management of chitin waste in the environment.

Comparative Genomics of Stenotrophomonas maltophilia and Stenotrophomonas rhizophila Revealed Characteristic Features of Both Species

Although Stenotrophomonas maltophilia strains are efficient biocontrol agents, their field applications have raised concerns due to their possible threat to human health. The non-pathogenic Stenotrophomonas rhizophila species, which is closely related to S. maltophilia, has been proposed as an alternative. However, knowledge regarding the genetics of S. rhizophila is limited. Thus, the aim of the study was to define any genetic differences between the species and to characterise their ability to promote the growth of plant hosts as well as to enhance phytoremediation efficiency. We compared 37 strains that belong to both species using the tools of comparative genomics and identified 96 genetic features that are unique to S. maltophilia (e.g., chitin-binding protein, mechanosensitive channels of small conductance and KGG repeat-containing stress-induced protein) and 59 that are unique to S. rhizophila (e.g., glucosylglycerol-phosphate synthase, cold shock protein with the DUF1294 domain, and pteridine-dependent dioxygenase-like protein). The strains from both species have a high potential for biocontrol, which is mainly related to the production of keratinases (KerSMD and KerSMF), proteinases and chitinases. Plant growth promotion traits are attributed to the biosynthesis of siderophores, spermidine, osmoprotectants such as trehalose and glucosylglycerol, which is unique to S. rhizophila. In eight out of 37 analysed strains, the genes that are required to degrade protocatechuate were present. While our results show genetic differences between the two species, they had a similar growth promotion potential. Considering the information above, S. rhizophila constitutes a promising alternative for S. maltophilia for use in agricultural biotechnology.