Long-term effects of sliver nanoparticles on the abundance and activity of soil microbiome

Silver nanoparticles（Ag NPs）are among the most extensively used engineered nanomaterials because of their wellestablished antimicrobial and unique physicochemical properties（Yin et al.,2015）.Applications of AgNPs have now been expanded beyond their initial use in medicine to industry, agriculture, and households.

Soil microbiomes divergently respond to heavy metals and polycyclic aromatic hydrocarbons in contaminated industrial sites

Contaminated sites from electronic waste(e-waste)dismantling and coking plants feature high concentrations of heavy metals(HMs)and/or polycyclic aromatic hydrocarbons(PAHs)in soil.Mixed contamination(HMsþPAHs)hinders land reclamation and affects the microbial diversity and function of soil microbiomes.In this study,we analyzed HM and PAH contamination from an e-waste dismantling plant and a coking plant and evaluated the influences of HM and PAH contamination on soil microbiomes.It was noticed that HMs and PAHs were found in all sites,although the major contaminants of the e-waste dismantling plant site were HMs(such as Cu at 5,947.58±433.44 mg kg^(-1),Zn at 4,961.38±436.51 mg kg^(-1),and Mn at 2,379.07±227.46 mg kg^(-1)),and the major contaminants of the coking plant site were PAHs(such as fluorene at 11,740.06±620.1 mg kg^(-1),acenaphthylene at 211.69±7.04 mg kg^(-1),and pyrene at 183.14±18.89 mg kg^(-1)).The microbiomes(diversity and abundance)of all sites were determined via high-throughput sequencing of 16S rRNA genes,and redundancy analysis was conducted to investigate the relations between soil microbiomes and contaminants.The results showed that the microbiomes of the contaminated sites divergently responded to HMs and PAHs.The abundances of the bacterial genera Sulfuritalea,Pseudomonas,and Sphingobium were positively related to PAHs,while the abundances of the bacterial genera Bryobacter,Nitrospira,and Steroidobacter were positively related to HMs.This study promotes an understanding of how soil microbiomes respond to single and mixed contamination with HMs and PAHs.

Microbial Responses of Soil Fertility to Depth of Tillage and Incorporation of Straw in a Haplic Chernozem in Northeast China

Straw is widely incorporated into soil worldwide,but most studies have concentrated on the effects of straw mulching or incorporation with topsoil.To determine the effect of depth of straw incorporation on bacterial and fungal communities,we established a field experiment in a region in Northeast China with Haplic Chernozems using four treatments:conventional tillage(CT,tillage to a depth of 15 cm with no straw incorporation),straw incorporation with conventional tillage(SCT,tillage to a depth of 15 cm),inversion tillage(IT,tillage to a depth of 35 cm)and straw incorporation with inversion tillage(SIT,tillage to a depth of 35 cm).The soils were managed by inversion to a depth of 15 or 35 cm after harvest.The results show that soil organic carbon content was significantly higher and pH and bulk density were significantly lower in the 15–35 cm layer in IT and SIT than CT and SCT.Fungal abundance was higher with straw incorporation,but fungal diversity was lower in the 0–15 cm layer in SCT and SIT than in CT and IT.Path length in the bacterial network was shorter and connectivity was higher in CT+SCT than in IT+SIT,leading to a more complex ecosystem,and the fungal network had opposite patterns.The key taxa in the phylum Actinobacteriota and Ascomycota in the microbial networks changed dramatically at the genus level following inversion tillage with straw amendment,which may increase bacterial network resistance to environmental disturbances and unstable fungal networks,resulting in large changes in the fungal community involved in the decomposition of recalcitrant straw-derived C and the more efficient acquisition of limiting resources.

Combined organic-inorganic fertilization builds higher stability of soil and root microbial networks than exclusive mineral or organic fertilization

Plant health and performance are highly dependent on the root microbiome.The impact of agricultural management on the soil microbiome has been studied extensively.However,a comprehensive understanding of how soil types and fertilization regimes affect both soil and root microbiome is still lacking,such as how fertilization regimes affect the root microbiome's stability,and whether it follows the same patterns as the soil microbiome.In this study,we carried out a longterm experiment to see how different soil types,plant varieties,and fertilizer regimens affected the soil and root bacterial communities.Our results revealed higher stability of microbial networks under combined organic-inorganic fertilization than those relied solely on inorganic or organic fertilization.The root microbiome variation was predominantly caused by total nitrogen,while the soil microbiome variation was primarily caused by pH and soil organic matter.Bacteroidetes and Firmicutes were major drivers when the soil was amended with organic fertilizer,but Actinobacteria was found to be enriched in the soil when the soil was treated with inorganic fertilizer.Our findings demonstrate how the soil and root microbiome respond to diverse fertilizing regimes,and hence contribute to a better understanding of smart fertilizer as a strategy for sustainable agriculture.

Global-scale analysis reveals distinct patterns of non-ribosomal peptide and polyketide synthase encoding genes in root and soil bacterial communities

Secondary metabolites(SMs)produced by soil bacteria,for instance antimicrobials and siderophores,play a vital role in bacterial adaptation to soil and root ecosystems and can contribute to plant health.Many SMs are non-ribosomal peptides and polyketides,assembled by non-ribosomal peptides synthetase(NRPS)and polyketide synthase(PKS)and encoded by biosynthetic gene clusters(BGCs).Despite their ecological importance,little is known about the occurrence and diversity of NRPs and PKs in soil.We extracted NRPS-and PKS-encodiing BGCs from 20 publicly available soil and root-associated metagenomes and annotated them using antiSMASH-DB.We found that the overall abundance of NRPSs and PKSs is similar in both environments,however NRPSs and PKSs were significantly clustered between soil and root samples.Moreover,the majority of identified sequences were unique to either soil-or root-associated datasets and had low identity to known BGCs,suggesting their novelty.Overall,this study illuminates the huge untapped diversity of predicted SMs in soil and root microbiomes,and indicates presence of specific SMs,which may play a role in inter-and intra-bacteriial interactions in root ecosystems.

Soil biofilms:microbial interactions,challenges,and advanced techniques for ex-situ characterization

Soil is inhabited by a myriad of microorganisms,many of which can form supracellular structures,called biofilms,comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival.Biofilms enable intensive inter-and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins.Here,we first discuss organization,dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome.Social interactions among bacteria,such as cooperation and competition,are discussed.We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms.Microfluidic platforms,which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with highthroughput screening and novel measurements,are also highlighted.This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.

Soil protists: An untapped microbial resource of agriculture and environmental importance

Protists are essential components of soil biodiversity and ecosystem functioning. They play a vital role in the microbial food web as consumers of bacteria, fungi, and other small eukaryotes and are also involved in maintaining soil fertility and plant productivity. Protists also contribute to regulating and shaping the bacterial community in terrestrial ecosystems via specific prey spectra. They play a role in plant growth promotion and plant health improvement,mostly via nutrient cycling, grazing, and the activation of bacterial genes required for plant growth and phytopathogen suppression. Thus, protists may prove to be a useful inoculant as biofertilizer and biocontrol agent. They can also be applied as model organisms as bioindicators of soil health. Despite their usefulness and essentiality, they are often forgotten and under-researched components of the soil microbiome, as most of our research focuses on bacteria and fungi. In this review, we provide an overview of the role of protists in plant productivity and plant health management and in shifts in soil bacterial community composition, as well as their roles as bioindicator. We also discuss the perspectives of knowledge gaps and future prospects to further improve soil biology.More research in soil protistology will provide insights into sustainable agriculture and environmental health alongside the study of bacteria and fungi.

Enrichment of bacteria involved in the nitrogen cycle and plant growth promotion in soil by sclerotia of rice sheath blight fungus

Rice sheath blight pathogen,Rhizoctonia solani,produces numerous sclerotia to overwinter.As a rich source of nutrients in the soil,sclerotia may lead to the change of soil microbiota.For this purpose,we amended the sclerotia of R.solani in soil and analyzed the changes in bacterial microbiota within the soil at different time points.At the phyla level,Proteobacteria,Acidobacteria,Bacteroidetes,Actinobacteria,Chloroflexi and Firmicutes showed varied abundance in the amended soil samples compared to those in the control.An increased abundance of ammonia-oxidizing bacterium(AOB)Nitrosospira and Nitrite oxidizing bacteria(NOB)i.e.,Nitrospira was observed,where the latter is reportedly involved in the nitrifier denitrification.Moreover,Thiobacillus,Gemmatimonas,Anaeromyxobacter and Geobacter,the vital players in denitrification,N2O reduction and reductive nitrogen transformation,respectively,depicted enhanced abundance in R.solani sclerotia-amended samples.Furthermore,asymbiotic nitrogen-fixing bacteria,notably,Azotobacter as well as Microvirga and Phenylobacterium with nitrogen-fixing potential also enriched in the amended samples compared to the control.Plant growth promoting bacteria,such as Kribbella,Chitinophaga and Flavisolibacter also enriched in the sclerotia-amended soil.As per our knowledge,this study is of its kind where pathogenic fungal sclerotia activated microbes with a potential role in N transformation and provided clues about the ecological functions of R.solani sclerotia on the stimulation of bacterial genera involved in different processes of N-cycle within the soil in the absence of host plants.

Rhizosphere immunity: targeting the underground for sustainable plant health management

Managing plant health is a great challenge formodern food production and is further complicated by thelack of common ground between the many disciplinesinvolved in disease control. Here we present the concept ofrhizosphere immunity, in which plant health is consideredas an ecosystem level property emerging from networks ofinteractions between plants, microbiota and the surround-ing soil matrix. These interactions can potentially extendthe innate plant immune system to a point where therhizosphere immunity can fulfil all four core functions ofafull immune system: pathogen prevention, recognition,response and homeostasis. We suggest that consideringplant health from a meta-organism perspective will help indeveloping multidisciplinary pathogen management stra-tegies that focus on steering the whole plant-microbe-soilnetworks instead of individual components. This might beachieved by bringing together the latest discoveries inphytopathology, microbiome research, soil science andagronomy to pave the way toward more sustainable andproductive agriculture.