Fundamentals and application in phytoremediation of an efficient arsenate reducing bacterium Pseudomonas putida ARS1

Arsenic is a ubiquitous environmental pollutant.Microbe-mediated arsenic biotransformations significantly infuence arsenic mobility and toxicity.Arsenic transformations by soil and aquatic organisms have been well documented,while little is known regarding effects due to endophytic bacteria.An endophyte Pseudomonas putida ARS1 was isolated from rice grown in arsenic contaminated soil.P.putida ARS1 shows high tolerance to arsenite(As(Ⅲ))and arsenate(As(V)),and exhibits efficient As(V)reduction and As(Ⅲ)effux activities.When exposed to 0.6 mg/L As(V),As(V)in the medium was completely converted to As(Ⅲ)by P.putida ARS1 within 4 hr.Genome sequencing showed that P.putida ARS1 has two chromosomal arsenic resistance gene clusters(arsRCBH)that contribute to efficient As(V)reduction and As(Ⅲ)effux,and result in high resistance to arsenicals.Wolffia globosa is a strong arsenic accumulator with high potential for arsenic phytoremediation,which takes up As(Ⅲ)more efficiently than As(V).Co-culture of P.putida ARS1 and W.globosa enhanced arsenic accumulation in W.globosa by 69%,and resulted in 91%removal of arsenic(at initial concentration of 0.6 mg/L As(V))from water within 3 days.This study provides a promising strategy for in situ arsenic phytoremediation through the cooperation of plant and endophytic bacterium.

Soil microbial ecology through the lens of metatranscriptomics

Metatranscriptomics is a cutting-edge technology for exploring the gene expression by,and functional activities of,the microbial community across diverse ecosystems at a given time,thereby shedding light on their metabolic responses to the prevailing environmental conditions.The double-RNA approach involves the simultaneous analysis of rRNA and mRNA,also termed structural and functional metatranscriptomics.By contrast,mRNA-centered metatranscriptomics is fully focused on elucidating community-wide gene expression profiles,but requires either deep sequencing or effective rRNA depletion.In this review,we critically assess the challenges associated with various experimental and bioinformatic strategies that can be applied in soil microbial ecology through the lens of functional metatranscriptomics.In particular,we demonstrate how recent methodological advancements in soil metatranscriptomics catalyze the development and expansion of emerging research fields,such as rhizobiomes,antibiotic resistomes,methanomes,and viromes.Our review provides a framework that will help to design advanced metatranscriptomic research in elucidating the functional roles and activities of microbiomes in soil ecosystems.

Utilization of human excrement in pre-modern China,its theoretical interpretations and ecological significance

The use of human excrement as fertilizer is a characteristic of traditional Chinese agriculture..The application of excrement from urban residents in agriculture since the Song Dynasty has ensured the cleanliness and hygiene of ancientChinesecities.As early as the Ming Dynasty,the Chinese people defined the principle of fertilizing fields with human excrement from the perspective of materialcirculation.The concept Peri-URban ecosystems(PURE)provides inspiration forurban-rural symbiosis regarding circulareconomy.The use of human excrement in fertilization is a major attribute differentiating the Chinese traditional agriculture from the agriculture in other regions around the world.Despite the fact that the exact record showing that human excrement was used as fertilizer in China emerged in the Western Han Dynasty(B.C.202-A.D.8),such records did not become prevalent until the Southern Song Dynasty(A.D.1127-1279).In the Ming and Qing eras(A.D.1368-1912),human excrement was even considered"top-class fertilizerand servedas themost essential fertilizerin farmland fertilization.The importance of human excrement in the Ming and Qing was mainly reflected by farmers'purchase of human excrement from urban areas.As fertilization practices became increasingly popular during the period,men of letters built a localized theoretical system centering on human excrement.Although the use of human excrement had both positive and negative impacts on public health and the ecological environment,the positive overshadowed the negativeas a whole.Today,it is worth pondering on how the utilization of human excrement as an agricultural resource can be improved so that a material cycle system can be rebuilt to re-connect the urban and rural areas.

Prevention and control strategies for antibiotic resistance:from species to community level

Antibiotic resistance genes(ARGs)and antibiotic resistant bacteria(ARB)in the environment pose serious threats to environmental security and public health.There is an urgent need for methods to specifically and effectively control environmental pollution or pathogen infection associated with ARGs and ARB.This review aims to provide an overview of methods abating the prevalence and spread of ARGs and ARB from species to community level.At the species level,species-specific technologies,such as nanoparticle-,photosensitizer-,CRISPR-Cas-,and phage-related technology can be utilized to clear a particular class of ARGs or ARB,and in combination with low-dose antibiotics,a higher removal efficiency can be achieved.Moreover,the combination of antibiotics can be used to reverse microbial resistance and treat recurrent antibiotic resistant pathogen infections.At the community level,community-specific strategies,such as biochar,hyperthermophilic compost,and fecal microbiota transplantation can eradicate most types of ARGs or ARB in one shot,reducing the probability of resistance development.Though some progress has been made to eliminate ARGs and ARB in disease treatment or decontamination scenarios,further research is still needed to elucidate their mechanisms of action and scopes of application,and efforts should be made to explore novel strategies to counter the prevalence of antibiotic resistance.

Collembolans maintain a core microbiome responding to diverse soil ecosystems

The unique gut habitat led to a core intestinal micro-biome in diverse soil ecosystems.The collembolan guts may help eliminate soil pathogens.Host-selection carried more weight on community assembly of gut microbiome.Soil invertebrates are widely distributed in the ecosystem and are essential for soil ecological processes.Inverte-brate gut microbiome plays an important role in host health and has been considered as a hidden microbial repository.However,little is known about how gut microbiome in soil invertebrates respond to diverse soil ecosystems.Based on a laboratory microcosm experiment,we characterized the assembling of microbiome of soil collembolans(Folsomia candida)from six representative regions of the soil ecosystem which they inhabit.Results showed that collembolan gut microbial communities differed significantly from their surrounding soil microbial communities.A dominant core gut microbiome was identified in gut habitat.Community analyses indicated that deterministic process dominated in the community assembly of collembolan gut microbiome.The results further demonstrate a dominant contribution of host selection in shaping gut microbiome.It is also worthy to mention that pathogens,such as common agricultural phytopathogenic fungi Fusarium,were involved in core microbiome,indicating that collembolans could act as vectors of pathogens.Our results unravelled the existence of gut core microbiome of collembolans in soil ecosystems and provided new insights for under-standing the crucial role of gut microbiome of soil fauna in maintaining microbial biodiversity and stability of soil ecosystems.

Harnessing the holobiont to alleviate the stress of aluminum toxicity to rice

Plant microbiome(including the microbiomes in the rhizosphere,phyllosphere,and endosphere)has been hailed as the second genome of the host,and plays a critical role in the health and fitness of the host.Similar to clinical medicine,microbiome transplant has been suggested to improve ecosystem restoration and crop production in degraded environment(Jurburg et al.,2022).This concept aligns with recent findings that emphasize the significant impact of soil and plant-associated microbiomes in agricultural productivity and the health of host plants(Wubs et al.,2016;Carthey et al.,2020;Mazza Rodrigues and Melotto,2023).

Bacterial biogeography in China and its association to land use and soil organic carbon

●6102 high-quality sequencing results of soil bacterial samples were re-analyzed.●The type of land use was the principal driver of bacterial richness and diversity.●SOC content is positively correlated with key bacteria and total nitrogen content.Soil organic carbon(SOC)is the largest pool of carbon in terrestrial ecosystems and plays a crucial role in regulating atmospheric CO_(2) concentrations.Identifying the essential relationship between soil bacterial communities and SOC concentration is complicated because of many factors,one of which is geography.We systematically re-analyzed 6102 high-quality bacterial samples in China to delineate the bacterial biogeographic distribution of bacterial communities and identify key species associated with SOC concentration at the continental scale.The type of land use was the principal driver of bacterial richness and diversity,and we used machine learning to calculate its influence on microbial composition and their co-occurrence relationship with SOC concentration.Cultivated land was much more complex than forest,grassland,wetland and wasteland,with high SOC concentrations tending to enrich bacteria such as Rubrobacter,Terrimonas and Sphingomona.SOC concentration was positively correlated with the amounts of soil total nitrogen and key bacteria Xanthobacteraceae,Streptomyces and Acidobacteria but was negatively correlated with soil pH,total phosphorus and Micrococcaceae.Our study combined the SOC pool with bacteria and indicated that specific bacteria may be key factors affecting SOC concentration,forcing us to think about microbial communities associated with climate change in a new way.

Gut microbiota research nexus:One Health relationshipbetween human,animal,and environmental resistomes

The emergence and rapid spread of antimicrobial resistance is of global public health concern.The gut microbiota harboring diverse commensal and opportunistic bacteria that can acquire resistance via horizontal and vertical gene transfers is considered an important reservoir and sink of antibiotic resistance genes(ARGs).In this review,we describe the reservoirs of gut ARGs and their dynamics in both animals and humans,use the One Health perspective to track the transmission of ARG-containing bacteria between humans,animals,and the environment,and assess the impact of antimicrobial resistance on human health and socioeconomic development.The gut resistome can evolve in an environment subject to various selective pressures,including antibiotic administration and environmental and lifestyle factors(e.g.,diet,age,gender,and living conditions),and interventions through probiotics.Strategies to reduce the abundance of clinically relevant antibiotic-resistant bacteria and their resistance determinants in various environmental niches are needed to ensure the mitigation of acquired antibiotic resistance.With the help of effective measures taken at the national,local,personal,and intestinal management,it will also result in preventing or minimizing the spread of infectious diseases.This review aims to improve our understanding of the correlations between intestinal microbiota and antimicrobial resistance and provide a basis for the development of management strategies to mitigate the antimicrobial resistance crisis.

Ecosystem Microbiome Science

The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms.To date,however,most microbiome studies have been carried out on individual hosts or particular environmental compartments.This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level.We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services.Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes,such as outbreaks of emerging infectious diseases or changes in mutualistic interactions.Despite enormous advances in microbial ecology,we are yet to study microbiomes of ecosystems as a whole.Doing so would establish a new framework for microbiome study:Ecosystem Microbiome Science.The advent and application of molecular and genomic technologies,together with data science and modeling,will accelerate progress in this field.

Tofu-a diet for human and planetary health

Ancient food cultures show a way to a more plant-based diet and may inspire a green transition in the food systems.

Advancing sustainable agriculture: Enhancing crop nutrition with next-generation nanotech-based fertilizers

The pressing need to enhance nutrient use efficiency(NUE)in fertilizers has become increasingly urgent in light of food insecurity and climate-related issues.Nanotechnology offers promising prospects for the development of effective and environmentally friendly alternatives in the field of fertilization.This review focuses on the impact of nanotechnology on conventional fertilizers,encompassing inorganic,organic,and microbial approaches.We emphasize the superior attributes of nano-fertilizers compared with their conventional counterparts and explore their potential and versatility in boosting crop productivity,reducing fertilizer expenses,and mitigating detrimental environmental impacts.In conclusion,given the significant challenges posed by food insecurity and climate change,the application of nano-fertilizers demonstrates immense potential for advancing sustainable and intelligent agricultural practices.

Urban agriculture as nature-based solutions:Three key strategies to tackle emerging issues on food security in Chinese cities under climatic and non-climatic challenges

1Introduction Achieving food and water security,according to the United Nations Sustainable Development Goals(SDGs),only requires a minimal environmental cost(Batalini de Macedo et al.,2022).However,in terms of agriculture,blindly devoting efforts to offset low-productivity farming or production techniques and industries,without systematic water,fertiliser,farm residue,tillage,and fallow management,will eventually interrupt the carbon sink under the soil and escalate greenhouse gas emissions,which is not helpful to meeting global climate targets.Thus,sciencebased land management practices are essential to decouple agricultural productivity from greenhouse gas emissions(Buscardo et al.,2021).

A new technique to ATTACK the silent pandemic of antimicrobial resistance

Due to the global proliferation of antibiotic‐resistant bacteria(ARB)and antibiotic resistance genes(ARGs)in humans,animals,and the environment,antibiotic resistance has become a silent pandemic threatening public health across the globe1.Anthropogenic activities,including clinical antibiotic use,intensive animal farming,and landfill waste,have been identified as the greatest risk factors for the dissemination of antibiotic resistance2,3.Additionally,the rise in disinfectant use during the COVID‐19 pandemic has exacerbated the situation by facilitating the spread of ARB4.Therefore,it is imperative to develop safe and effective strategies to combat this silent pandemic.These strategies must focus on reducing the presence of ARB and ARGs in the environment while also accelerating the implementation of the“ONE EARTH,ONE HEALTH”action plan.

Gene Structure and Expression of the High-affinity Nitrate Transport System in Rice Roots

Rice has a preference for uptake of ammonium over nitrate and can use ammonium-N efficiently. Consequently, transporters mediating ammonium uptake have been extensively studied, but nitrate transporters have been largely ignored. Recently, some reports have shown that rice also has high capacity to acquire nitrate from growth medium, so understanding the nitrate transport system in rice roots is very important for improving N use efficiency in rice. The present study Identified four putative NRT2 and two putative NAR2 genes that encode components of the high-affinity nitrate transport system （HATS） in the rice （Oryza sativa L. subsp, japonica cv. Nipponbare） genome. OsNRT2.1 and OsNRT2.2 share an Identical coding region sequence, and their deduced proteins are closely related to those from mono-cotyledonous plants. The two NAR2 proteins are closely related to those from mono-cotyledonous plants as well. However, OsNRT2.3 and OsNRT2.4 are more closely related to Arabidopsis NRT2 proteins. Relative quantitative reverse trsnscription-polymerase chain reaction analysis showed that all of the six genes were rapidly upregulated and then downrsgulated in the roots of N-starved rice plants after they were re-supplied with 0.2 mM nitrate, but the response to nitrate differed among gene members. The results from phylogenetic tree, gene structure and expression analysis implied the divergent roles for the Individual members of the rice NRT2 and NAR2 families. High-affinity nitrate influx rates associated with nitrate induction in rice roots were investigated and were found to be regulated by external pH. Compared with the nitrate influx rates at pH 6.5, alkaline pH （pH 8.0） inhibited nitrate influx, and acidic pH （pH 5.0） enhanced the nitrate influx in 1 h nitrate induced roots, but did not significantly affect that in 4 to 8 h nitrate induced roots.

A buried Neolithic paddy soil reveals loss of microbial functional diversity after modern rice cultivation

It has been documented that human activities are causing the rapid loss of taxonomic, phylogenetic, genetic and functional diversity in soils. However, it remains unclear how modern intensive rice cultivation impacts the soil microbiome and its functionality. Here we examined the microbial composition and function differences between a buried Neolithic paddy soil and an adjacent, currently-cultivated paddy soil using high throughput metagenomics technologies. Our results showed that the currently cultivated soil contained about 10-fold more microbial biomass than the buried one. Analyses based on both 16S rRNA genes and functional gene array showed that the currently cultivated soil had significantly higher phylogenetic diversity, but less functional diversity than the buried Neolithic one. The community structures were significantly different between modern and ancient soils, with functional structure shifting towards accelerated organic carbon （C） degradation and nitrogen （N） transfor- mation in the modem soils. This study implies that, modern intensive rice cultivation has substantially altered soil microbial functional structure, leading to functional homogenization and the promotion of soil ecological functions related to the acceleration of nutrient cycling which is necessary for high crop yields.

Regulation of the High-Affinity Nitrate Transport System in Wheat Roots by Exogenous Abscisic Acid and Glutamine

Nitrate is a major nitrogen （N） source for most crops. Nitrate uptake by root cells is a key step of nitrogen metabolism and has been widely studied at the physiological and molecular levels. Understanding how nitrate uptake is regulated will help us engineer crops with improved nitrate uptake efficiency. The present study investigated the regulation of the high-affinity nitrate transport system （HATS） by exogenous abscisic acid （ABA） and glutamine （Gin） in wheat （Triticum aestivum L.） roots. Wheat seedlings grown in nutrient solution containing 2 mmol/L nitrate as the only nitrogen source for 2weeks were deprived of N for 4d and were then transferred to nutrient solution containing 50 μmol/L ABA, and 1 mmol/L Gin in the presence or absence of 2 mmol/L nitrate for 0, 0.5, 1, 2, 4, and 8 h. Treated wheat plants were then divided into two groups. One group of plants was used to investigate the mRNA levels of the HATS components NRT2 and NAR2 genes in roots through semi-quantitative RT-PCR approach, and the other set of plants were used to measure high-affinity nitrate influx rates in a nutrient solution containing 0.2 mmol/L ^15N-labeled nitrate. The results showed that exogenous ABA induced the expression of the TaNRT2.1, TaNRT2.2, TaNRT2.3, TaNAR2.1, and TaNAR2.2 genes in roots when nitrate was not present in the nutrient solution, but did not further enhance the induction of these genes by nitrate. Glutamine, which has been shown to inhibit the expression of NRT2 genes when nitrate is present in the growth media, did not inhibit this induction. When Gin was supplied to a nitrate-free nutrient solution, the expression of these five genes in roots was induced. These results imply that the inhibition by Gin of NRT2 expression occurs only when nitrate is present in the growth media. Although exogenous ABA and Gin induced HATS genes in the roots of wheat, they did not induce nitrate influx.

Introgression of Resistance to Powdery Mildew Conferred by Chromosome 2R by Crossing Wheat Nullisomic 2D with Rye

Using the nulUsomic back-cross procedure, four wheat-rye chromosome substitution 2R （2D） lines with different agronomic performance, designated WR02-145-1, WR01-145-2, WR02-145-3, and WR02-145-4, were produced from a cross between 2D nullisomic wheat （Triticum aestivum L. cv. ＂Xiaoyan 6＂） and rye （Secale cereale L. cv. ＂German White＂）. The chromosomal constitution of 2n=42=21 in WR02-145 lines was confirmed by cytological and molecular cytogenetic methods. Using genomic in situ hybridization on root tip chromosome preparations, a pair of intact rye chromosomes was detected in the WR02-145 lines. PCR using chromosome-specific primers confirmed the presence of 2R chromosomes of rye in these wheat-rye lines, indicating that WR02o145 lines are disomic chromosome substitution lines 2R （2D）. The WR02-145 lines are resistant to the powdery mildew （Erysiphe graminis DC. f. sp. tritici E. Marchal） isolates prevalent in northern China and may possess gene（s） for resistance to powdery mildew, which differ from the previously identified Pm7gene located on chromosome 2RL. The newly developed ＂Xiaoyan 6＂- ＂German White＂ 2R （2D） chromosome substitution lines are genetically stable, show desirable agronomic traits, and are expected to be useful in wheat improvement.

Loss of soil microbial diversity exacerbates spread of antibiotic resistance

Loss of biodiversity is a major threat to the ecosystem processes upon which society depends.Natural ecosystems differ in their resistance to invasion by alien species,and this resistance can depend on the diversity in the system.Little is known,however,about the barriers that microbial diversity provides against microbial invasion.The increasing prevalence of antibioticresistant bacteria is a serious threat to public health in the 21st century.We explored the consequences of the reduction in soil microbial diversity for the dissemination of antibiotic resistance.The relationship between this diversity and the invasion of antibiotic resistance was investigated using a dilution-to-extinction approach coupled with high-capacity quantitative PCR.Microbial diversity was negatively correlated with the abundance of antibiotic-resistance genes,and this correlation was maintained after accounting for other potential drivers such as incubation time and microbial abundance.Our results demonstrate that high microbial diversity can act as a biological barrier resist the spread of antibiotic resistance.These results fill a critical gap in our understanding of the role of soil microbial diversity in the health of ecosystems.

Collembolans accelerate the dispersal of antibiotic resistance genes in the soil ecosystem

Soils have become an important sink for antibiotic resistance genes(ARGs).To better understand the impacts of ARGs on the soil ecosystem,the transport of ARGs is a basic question.So far,however,the role of soil animals in the dispersal of ARGs is not understood.Here,two treatments(without collembolans and with collembolans)were established,each treatment included unamended and manure-amended soil,and soil samples were collected at 14,28 and 56 days after incubation.The effects of the collembolan Folsomia candida on dispersal of ARGs in the soil ecosystem were explored using high-throughput qPCR combined with Illumina sequencing.As the culture time increased,more shared ARGs and OTUs were detected between the unamended and manured soil,especially in the treatment with collembolans.Vancomycin,aminoglycoside and MLSB genes may have been more readily transported by the collembolan.On the 28th day after incubation,a high abundance of mobile genetic elements(MGEs)was found in the treatment with collembolans.These results clearly reveal that collembolans can accelerate the dispersal of ARGs in the soil ecosystem.Procrustes analysis and the Mantel test both indicate that soil bacterial communities were significantly correlated with ARG profiles.Furthermore,partial redundancy analysis indicates that soil bacterial communities can explain 41.28% of the variation in ARGs.These results suggest that the change of soil microbial community have an important contribution to the dispersal of ARGs by the collembolan.

Soil inorganic carbon sequestration through alkalinity regeneration using biologically induced weathering of rock powder and biochar

Soil inorganic carbon(SIC)accounts for about half of the C reserves worldwide and is considered more stable than soil organic carbon(SOC).However,soil acidification,driven mainly by nitrogen(N)fertilization can accelerate SIC losses,possibly leading to complete loss under continuous and intensive N fertilization.Carbonate-free soils are less fertile,productive,and more prone to erosion.Therefore,minimizing carbonate losses is essential for soil health and climate change mitigation.Rock/mineral residues or powder have been suggested as a cheaper source of amendments to increase soil alkalinity.However,slow mineral dissolution limits its efficient utilization.Soil microorganisms play a vital role in the weathering of rocks and their inoculation with mineral residues can enhance dissolution rates.Biochar is an alternative material for soil amendments,in particular,bone biochar(BBC)contains higher Ca and Mg that can induce even higher alkalinity.This review covers i)the contribution and mechanism of rock residues in alkalinity generation,ii)the role of biochar or BBC to soil alkalinity,and iii)the role of microbial inoculation for accelerating alkalinity generation through enhanced mineral dissolution.We conclude that using rock residues/BBC combined with microbial agents could mitigate soil acidification and SIC losses and also improve agricultural circularity.