Composition identification and functional verification of bacterial community in disease-suppressive soils by machine learning

Plant-Driven Assembly of Disease-Suppressive Soil Microbiomes

Plants have coevolved together with the microbes that surround them and this assemblage of host and microbes functions as a discrete ecological unit called a holobiont. This review outlines plant-driven assembly of disease-suppressive microbiomes. Plants are colonized by microbes from seed, soil, and air but selectively shape the microbiome with root exudates, creating microenvironment hot spots where microbes thrive. Using plant immunity for gatekeeping and surveillance, host-plant genetic properties govern microbiome assembly and can confer adaptive advantages to the holobiont. These advantages manifest in disease-suppressive soils, where buildup of specific microbes inhibits the causal agent of disease, that typically develop after an initial disease outbreak. Based on disease-suppressive soils such as take-all decline, we developed a conceptual model of how plants in response to pathogen attack cry for help and recruit plant-protective microbes that confer increased resistance. Thereby, plants create a soilborne legacy that protects subsequent generations and forms disease-suppressive soils.

Engineering agricultural soil microbiomes and predicting plant phenotypes

Plant growth-promoting rhizobacteria (PGPR) can improve crop yields, nutrient use efficiency, plant tolerance to stressors, and confer benefits to future generations of crops grown in the same soil. Unlocking the potential of microbial communities in the rhizosphere and endosphere is therefore of great interest for sustainable agriculture advancements. Before plant microbiomes can be engineered to confer desirable phenotypic effects on their plant hosts, a deeper understanding of the interacting factors influencing rhizosphere community structure and function is needed. Dealing with this complexity is becoming more feasible using computational approaches. In this review, we discuss recent advances at the intersection of experimental and computational strategies for the investigation of plant-microbiome interactions and the engineering of desirable soil microbiomes.

Embracing complexity in plant-microbiome systems

Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.

Unveiling the frontiers of potato disease research through bibliometric analysis

Research on potato diseases had been widely reported, but a systematic review of potato diseases was lacking. Here, bibliometrics was used to systematically analyze the progress of potato disease. The publications related to "potato" and "disease" were searched in the Web of Science (WOS) from 2014 to 2023. The results showed that a total of 2095 publications on potato diseases were retrieved, with the annual publication output increasing year by year at a growth rate of 8.52%. The main countries where publications were issued were the United States, China, and India. There was relatively close cooperation observed between China, the United States, and the United Kingdom in terms of international collaboration, while international cooperation by India was less extensive. Based on citation analysis and trending topics, potential future research directions include nanoparticles, which provides highly effective carriers for biologically active substances due to their small dimensions, extensive surface area, and numerous binding sites; machine learning, which facilitates rapid identification of relevant targets in extensive datasets, thereby accelerating the process of disease diagnosis and fungicide innovation; and synthetic communities composed of various functional microorganisms, which demonstrate more stable effects in disease prevention and control.

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness

Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.

IMPORTANCE

Ralstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.

Phages in different habitats and their ability to carry antibiotic resistance genes

As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere

Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

Root rot destabilizes the Sanqi rhizosphere core fungal microbiome by reducing the negative connectivity of beneficial microbes

The stability of microbial communities, especially among core taxa, is essential for supporting plant health. However, the impacts of disease infection on the stability of rhizosphere fungal core microbiome remain largely unexplored. In this study, we delved into the effects of root rot infestation on the community structure, function, network complexity, and stability of Sanqi fungal core microbiomes, employing amplicon sequencing combined with co-occurrence network and cohesion analyses. Our investigation revealed that root rot disease led to a decrease in the α-diversity but an increase in the β-diversity of the Sanqi fungal core microbiomes in the rhizosphere. Notably, Ilyonectria, Plectosphaerella, and Fusarium emerged as indicator species in the rhizosphere core microbiome of root rot-infected Sanqi plants, while Mortierella predominated as the dominant biomarker taxa in healthy soils. Additionally, root rot diminished the complexity and modularity of the rhizosphere networks by reducing the metrics associated with nodes, edges, degrees, and modularity. Furthermore, root rot resulted in a reduction in the proportion of negative connections in the network and the negative/positive cohesion of the entire core fungal microbiome. Particularly noteworthy was the observation that root rot infection destabilized the rhizosphere core fungal microbiome by weakening the negative connectivity associated with beneficial agents. Collectively, these results highlight the significance of the negative connectivity of beneficial agents in ensuring the stability of core microbial community.IMPORTANCERoot rot disease has been reported as the most devastating disease in the production process of artificial cultivated Sanqi ginseng, which seriously threatens the Sanqi industry. This study provides valuable insights into how root rot influences microbial relationships within the community. These findings open up opportunities for disease prevention and the promotion of plant health by regulating microbial interactions. In summary, the research sheds light on the ecological consequences of root rot on rhizosphere fungal microbiomes and offers potential strategies for managing soil-borne diseases and enhancing plant health.

Long-Term Field Application of a Plant Growth-Promoting Rhizobacterial Consortium Suppressed Root-Knot Disease by Shaping the Rhizosphere Microbiota

Root-knot nematodes (Meloidogyne spp.) are one of the most economically important plant parasitic nematodes, infecting almost all cultivated plants and resulting in severe yield losses every year. Plant growth-promoting rhizobacteria (PGPR) have been extensively used to prevent and control root-knot diseases and increase yield. In this study, the effect of a consortium of three PGPR strains (Bacillus cereus AR156, B. subtilis SM21, and Serratia sp. XY21; hereafter "BBS") on root-knot disease of cucumber was evaluated. The application of BBS significantly reduced the severity of root-knot disease by 56 to 72%, increased yield by 36 to 55%, and improved fruit quality by 14 to 90% and soil properties by 1 to 90% relative to the control in the cucumber fields of the Nanjing suburb, Jiangsu Province, from 2015 to 2018. BBS altered the rhizosphere bacterial community. Compared with the control group, it significantly (false discovery rate, P < 0.05) increased the abundance of 14 bacterial genera that were negatively correlated with disease severity. Additionally, the redundancy analysis suggested that BBS-treated rhizosphere soil samples were dominated by disease-suppressive bacteria, including the genera Iamia, Kutzneria, Salinibacterium, Mycobacterium, Kribbella, Pseudonocardia, Sporichthya, Sphaerisporangium, Actinomadura, Flavisolibacter, Phenylobacterium, Bosea, Hyphomicrobium, Agrobacterium, Sphingomonas, and Nannocystis, which were positively related to total organic carbon, total nitrogen, total organic matter, dissolved organic carbon, [Formula: see text]-N, and available phosphorus contents. This suggests that BBS suppresses root-knot nematodes and improves the soil chemical properties of cucumber by altering the rhizosphere microbial community.

Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning

Plant-associated microbiomes contribute to important ecosystem functions such as host resistance to biotic and abiotic stresses. The factors that determine such community outcomes are inherently difficult to identify under complex environmental conditions. In this study, we present an experimental and analytical approach to explore microbiota properties relevant for a microbiota-conferred host phenotype, here plant protection, in a reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification and regression analyses as well as empirical validation to test potential explanatory factors of community structure and composition, including evenness, total commensal colonization, phylogenetic diversity, and strain identity. We find strain identity to be the most important predictor of pathogen reduction, with machine learning algorithms improving performances compared to random classifications (94-100% versus 32% recall) and non-modelled predictions (0.79-1.06 versus 1.5 RMSE). Further experimental validation confirms three strains as the main drivers of pathogen reduction and two additional strains that confer protection in combination. Beyond the specific application presented in our study, we provide a framework that can be adapted to help determine features relevant for microbiota function in other biological systems.

Soterobionts: disease-preventing microorganisms and proposed strategies to facilitate their discovery

Crop production and the food security that it provides are currently threatened worldwide by plant pathogens. Conventional control measures, such as breeding for resistant plants, are progressively losing their efficacy due to rapidly evolving pathogens. The plant microbiota contributes to essential functions of host plants, among which is protection against pathogens. Only recently, microorganisms that provide holistic protection against certain plant diseases were identified. They were termed as 'soterobionts' and extend their host's immune system, which results in disease-resistant phenotypes. Further exploration of such microorganisms could not only provide answers to better understand the implications of the plant microbiota in health and disease, but also contribute to new developments in agriculture and beyond. The aim of this work is to point out how the identification of plant-associated soterobionts can be facilitated, and to discuss technologies that will be required to enable this.

Large-scale comparative analysis reveals different bacterial community structures in full- and lab-scale wastewater treatment bioreactors

The activated sludge process is widely used for biological wastewater treatment due to its low cost and high efficiency. Although numerous lab-scale bioreactor experiments have been conducted to investigate the microorganism performance and mechanisms in activated sludge, understanding the bacterial community differences between full- and lab-scale bioreactors has remained elusive. In this study, we investigated the bacterial communities in 966 activated sludge samples obtained from various bioreactors, including both full- and lab-scale ones, from 95 previous studies. Our findings reveal significant differences in the bacterial communities between full- and lab-scale bioreactors, with thousands of bacterial genera exclusive to each scale. We also identified 12 genera that are frequently abundant in full-scale bioreactors but rarely observed in lab-scale reactors. By using a machine-learning method, organic matter and temperature were determined as the primary factors affecting microbial communities in full- and lab-scale bioreactors. Additionally, transient bacterial species from other environments may also contribute to the observed bacterial community differences. Furthermore, the bacterial community differences between full- and lab-scale bioreactors were verified by comparing the results of lab-scale bioreactor experiments to full-scale bioreactor sampling. Overall, this study sheds light on the bacteria overlooked in lab-scale studies and deepens our understanding of the differences in bacterial communities between full- and lab-scale bioreactors.

Does straw returning affect the root rot disease of crops in soil? A systematic review and meta-analysis

Straw returning is a sustainable way that does not destroy soil ecology in agronomic management. Some studies have found that straw returning may aggravate or reduce soilborne diseases in the past few decades. Despite the increasing number of independent studies investigated the effect of straw returning on root rot of crops, the quantitative analysis regarding the relationship between straw returning and crop root rot is still undefined. In this study, keywords co-occurrence matrix was extracted from 2489 published studies (published from 2000 to 2022, the same below) on controlling soilborne diseases of crops. The methods used for soilborne diseases prevention have shifted from chemical to biological and agricultural control since 2010. As root rot is the soilborne disease with the largest weight in keyword co-occurrence according to statistics, we further collected 531 articles focusing on crop root rot. Notably, the 531 studies are mainly distributed in the United States, Canada, China and other countries in Europe and the south and southeast of Asia, and focus on the root rot of soybean, tomato, wheat and other important grain crops or economic crops. Based on the meta-analysis of 534 measurements in 47 previous studies, we explored how 10 management factors (soil pH/texture, type/size of straw, depth/rate/cumulative amount of application, days after application, beneficial/pathogenic microorganism inoculated before application and annual N-fertilizer input) during straw returning affect root rot onset worldwide. The results showed that straw size and microorganisms inoculated before straw returning are the key factors affecting the incidence of root rot. In combination with actual agricultural production, detailed advice applicable to traditional farming system on the optimization management of straw returning was given. This study emphasized the significance of straw pretreatment and farmland management to reduce soilborne diseases during straw returning.

Global distribution of marine microplastics and potential for biodegradation

Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea. However, the limited number of samples hindered our prediction, a priority issue that needs to be addressed in the future. We further identified hosts with microplastic degradation genes (MDGs) and found that Proteobacteria accounted for a high proportion of MDG hosts, mainly Alphaproteobacteria and Gammaproteobacteria, with host-specific patterns. Our study is essential for raising awareness, identifying areas with microplastic pollution, providing a prediction method of machine learning to prioritize surveillance, and identifying the global potential of marine microbiomes to degrade microplastics, providing a reference for selecting bacteria that have the potential to degrade microplastics for further applied research.

Rhizosphere bacterial interactions and impact on plant health

The rhizosphere is a chemically complex environment that harbors a strikingly diverse microbial community. The past few decades have seen a rapid growth in the body of literature on plant-microbe-microbe interactions and plant health. Thus, the aim of this paper is to review current knowledge on plant-microbe-microbe (specifically bacteria) interactions in the rhizosphere and how these influence rhizosphere microbiomes and impact plant health. This article discusses (i) how the plant recruits beneficial rhizosphere bacteria and ii) how competition between rhizosphere bacteria and mechanisms/weapons employed in bacteria-bacteria competition shapes rhizosphere microbiome and in turn affects plant heath. The discussion mainly focuses on interference competition, characterized by production of specialized metabolites (antibacterial compounds) and exploitative competition where a bacterial strain restricts the competitor's access to nutrients such as through secretion of siderophores that could allude to cooperation. Understanding mechanisms employed in bacteria-bacteria and plant-bacteria interactions could provide insights into how to manipulate microbiomes for improved agricultural outcomes.

Detection, Diagnosis, and Preventive Management of the Bacterial Plant Pathogen Pseudomonas syringae

Plant diseases caused by the pathogen Pseudomonas syringae are serious problems for various plant species worldwide. Accurate detection and diagnosis of P. syringae infections are critical for the effective management of these plant diseases. In this review, we summarize the current methods for the detection and diagnosis of P. syringae, including traditional techniques such as culture isolation and microscopy, and relatively newer techniques such as PCR and ELISA. It should be noted that each method has its advantages and disadvantages, and the choice of each method depends on the specific requirements, resources of each laboratory, and field settings. We also discuss the future trends in this field, such as the need for more sensitive and specific methods to detect the pathogens at low concentrations and the methods that can be used to diagnose P. syringae infections that are co-existing with other pathogens. Modern technologies such as genomics and proteomics could lead to the development of new methods of highly accurate detection and diagnosis based on the analysis of genetic and protein markers of the pathogens. Furthermore, using machine learning algorithms to analyze large data sets could yield new insights into the biology of P. syringae and novel diagnostic strategies. This review could enhance our understanding of P. syringae and help foster the development of more effective management techniques of the diseases caused by related pathogens.

The Golden Goal of Soil Management: Disease-Suppressive Soils

Disease-suppressive soils encompass specific plant-pathogen-microbial interactions and represent a rare example of an agroecosystem where soil conditions and microbiome together prevent the pathogen from causing disease. Such soils have the potential to serve as a model for characterizing soil pathogen-related aspects of soil health, but the mechanisms driving the establishment of suppressive soils vary and are often poorly characterized. Yet, they can serve as a resource for identifying markers for beneficial activities of soil microorganisms concerning pathogen prevention. Many recent studies have focused on the nature of disease-suppressive soils, but it has remained difficult to predict where and when they will occur. This review outlines current knowledge on the distribution of these soils, soil manipulations leading to pathogen suppression, and markers including bacterial and fungal diversity, enzymes, and secondary metabolites. The importance to consider soil legacy in research on the principles that define suppressive soils is also highlighted. The goal is to extend the context in which we understand, study, and use disease-suppressive soils by evaluating the relationships in which they occur and function. Finally, we suggest that disease-suppressive soils are critical not only for the development of indicators of soil health, but also for the exploration of general ecological principles about the surrounding landscape, effects of deeper layers of the soil profile, little studied soil organisms, and their interactions for future use in modern agriculture.

Shaping effects of rice, wheat, maize, and soybean seedlings on their rhizosphere microbial community

The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops.

Seasonal Shifts in Bacterial Community Structures in the Lateral Root of Sugar Beet Grown in an Andosol Field in Japan

To investigate functional plant growth-promoting rhizobacteria in sugar beet, seasonal shifts in bacterial community structures in the lateral roots of sugar beet were examined using amplicon sequencing ana-lyses of the 16S rRNA gene. Shannon and Simpson indexes significantly increased between June and July, but did not significantly differ between July and subsequent months (August and September). A weighted UniFrac principal coordinate ana-lysis grouped bacterial samples into four clusters along with PC1 (43.8%), corresponding to the four sampling months in the order of sampling dates. Taxonomic ana-lyses revealed that bacterial diversity in the lateral roots was exclusively dominated by three phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) in all samples examined. At the lower taxonomic levels, the dominant taxa were roughly classified into three groups. Therefore, the relative abundances of seven dominant genera (Janthinobacterium, Kribbella, Pedobacter, Rhodanobacter, Sphingobium, Sphingopyxis, and Streptomyces) were the highest in June and gradually decreased as sugar beet grew. The relative abundances of eight taxa (Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Novosphingobium, Phyllobacteriaceae, Pseudomonas, Rhizobiaceae, and Sphingomonas) were mainly high in July and/or August. The relative abundances of six taxa (unclassified Comamonadaceae, Cytophagaceae, unclassified Gammaproteobacteria, Haliangiaceae, unclassified Myxococcales, and Sinobacteraceae) were the highest in September. Among the dominant taxa, 12 genera (Amycolatopsis, Bradyrhizobium, Caulobacter, Devosia, Flavobacterium, Janthinobacterium, Kribbella, Kutzneria, Pedobacter, Rhizobium, Rhodanobacter, and Steroidobacter) were considered to be candidate groups of plant growth-promoting bacteria based on their previously reported beneficial traits as biopesticides and/or biofertilizers.

Negative effects of abamectin on soil microbial communities in the short term

With the widespread use of abamectin in agriculture, there is increasing urgency to assess the effects of abamectin on soil microorganisms. Here, we treated plant-soil microcosms with abamectin at concentrations of 0.1 and 1.0 mg/kg and quantified the impacts of abamectin on bulk and rhizosphere soil microbial communities by shotgun metagenomics after 7 and 21 days of exposure. Although abamectin was reported to be easily degradable, it altered the composition of the soil microbial communities, disrupted microbial interactions, and decreased community complexity and stability after 7 days of exposure. After treatment with abamectin at a concentration of 1.0 mg/kg, some opportunistic human diseases, and soil-borne pathogens like Ralstonia were enriched in the soil. However, most ecological functions in soil, particularly the metabolic capacities of microorganisms, recovered within 21 days after abamectin treatment. The horizontal and vertical gene transfer under abamectin treatments increased the levels of antibiotic resistance genes dissemination. Overall, our findings demonstrated the negative effects of abamectin on soil ecosystems in the short-term and highlight a possible long-term risk to public and soil ecosystem health associated with antibiotic resistance genes dissemination.

Biosurfactant Production by Bacillus amyloliquefaciens C11 and Streptomyces lavendulae C27 Isolated from a Biopurification System for Environmental Applications

Biosurfactant-producing bacteria can be found in contaminated environments such as biopurification systems (BPS) for pesticide treatments. A total of 18 isolates were screened to determine their ability to produce extracellular biosurfactants, using olive oil as the main carbon source. Out of the eighteen isolates, two strains (C11 and C27) were selected for biosurfactant production. The emulsification activities of the C11 and C27 strains using sunflower oil was 58.4 and 53.7%, respectively, and 46.6 and 48.0% using olive oil. Using molecular techniques and MALDI-TOF, the strains were identified as Bacillus amyloliquefaciens (C11) and Streptomyces lavendulae (C27). The submerged cultivation of the two selected strains was carried out in a 1 L stirred-tank bioreactor. The maximum biosurfactant production, indicated by the lowest surface tension measurement, was similar (46 and 45 mN/m) for both strains, independent of the fact that the biomass of the B. amyloliquefaciens C11 strain was 50% lower than the biomass of the S. lavendulae C27 strain. The partially purified biosurfactants produced by B. amyloliquefaciens C11 and S. lavendulae C27 were characterized as a lipopeptide and a glycolipid, respectively. These outcomes highlight the potential of the selected biosurfactant-producing microorganisms for improving pesticides’ bioavailability and therefore the degradational efficacy of BPS.

Characterization of the Soil Bacterial Community from Selected Boxwood Gardens across the United States

In a recent study, we observed a rapid decline of the boxwood blight pathogen Calonectria pseudonaviculata (Cps) soil population in all surveyed gardens across the United States, and we speculated that these garden soils might be suppressive to Cps. This study aimed to characterize the soil bacterial community in these boxwood gardens. Soil samples were taken from one garden in California, Illinois, South Carolina, and Virginia and two in New York in early summer and late fall of 2017 and 2018. Soil DNA was extracted and its 16S rRNA amplicons were sequenced using the Nanopore MinION® platform. These garden soils were consistently dominated by Rhizobiales and Burkholderiales, regardless of garden location and sampling time. These two orders contain many species or strains capable of pathogen suppression and plant fitness improvement. Overall, 66 bacterial taxa were identified in this study that are known to have strains with biological control activity (BCA) against plant pathogens. Among the most abundant were Pseudomonas spp. and Bacillus spp., which may have contributed to the Cps decline in these garden soils. This study highlights the importance of soil microorganisms in plant health and provides a new perspective on garden disease management using the soil microbiome.

Microbial polyketides and their roles in insect virulence: from genomics to biological functions

Covering: May 1966 up to January 2022Entomopathogenic microorganisms have potential for biological control of insect pests. Their main secondary metabolites include polyketides, nonribosomal peptides, and polyketide-nonribosomal peptide (PK-NRP) hybrids. Among these secondary metabolites, polyketides have mainly been studied for structural identification, pathway engineering, and for their contributions to medicine. However, little is known about the function of polyketides in insect virulence. This review focuses on the role of bacterial and fungal polyketides, as well as PK-NRP hybrids in insect infection and killing. We also discuss gene distribution and evolutional relationships among different microbial species. Further, the role of microbial polyketides and the hybrids in modulating insect-microbial symbiosis is also explored. Understanding the mechanisms of polyketides in insect pathogenesis, how compounds moderate the host-fungus interaction, and the distribution of PKS genes across different fungi and bacteria will facilitate the discovery and development of novel polyketide-derived bio-insecticides.

Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts

The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.

Effects of ofloxacin on the structure and function of freshwater microbial communities

Ofloxacin (OFL) is a broad-spectrum fluoroquinolone antibiotic frequently used in clinic for treating bacterial infections. The discharged OFL would inevitably enter into aquatic ecosystems, affecting the growth of non-target microorganisms, which may result in micro-ecosystem imbalance. To the best of our knowledge, researches in this area are rather sparse. The present study evaluated the response of photosynthetic microorganisms (cyanobacteria, eukaryotic algae) and aquatic microbial community to OFL in a microcosm. Results showed that ofloxacin presented an inhibitory effect on the growth Microcystis aeruginosa. Although 0.1 mg/L OFL has no significant impact on alpha diversity of the microbial communities, it obviously altered the structure and decreased the species interaction of prokaryotic community by reducing the capacities of nitrogen fixation, photosynthetic and metabolic capacity of the microbial community. This study pointed out that the residual OFL in water would disturb the balance of the aquatic micro-ecology, suggesting that more attentions should be given to the negative effects of antibiotics and other bioactive pollutants on aquatic environments.