Microbiomes in agroecosystem: Diversity, function and assembly mechanisms

The contrasting roles of fungal and bacterial diversity and composition in shaping the multifunctionality of rhizosphere and bulk soils across large-scale bamboo forests

Soil microbes regulate nutrient cycling, organic matter decomposition, and other processes, thereby maintaining soil multifunctionality (SMF). However, the relationship between microbial characteristics and soil multifunctionality has primarily been studied in bulk soils, with less attention to rhizosphere soils. Moreover, this relationship remains unclear within a single forest type across large scales. In this study, we selected six sites across the distribution range of moso bamboo (Phyllostachys edulis (Carrière) J. Houz.) in China to quantify the relationship between microbial communities and soil multifunctionality in both rhizosphere and bulk soil, and to evaluate how abiotic factors influence this relationship. Our results showed that microbial diversity was negatively correlated with SMF, while the key microbial drivers (bacteria or fungi) of SMF varied between soil compartments (i.e., rhizosphere and bulk soil). Soil variables influenced SMF in bulk soils by affecting bacterial diversity and fungal composition, whereas in rhizosphere soils, soil variables influenced SMF primarily by affecting fungal diversity and composition, suggesting that different characteristics of bacterial and fungal communities drive SMF. Climatic factors exert a more significant influence on the multifunctionality of rhizosphere soils compared to bulk soils. Considering the intricate interplay between plants and soil microbes, our study highlights the importance of integrating SMF and microbial community structure within distinct soil compartments.

Plant-microbiome interactions and their impacts on plant adaptation to climate change

Plants have co-evolved with a wide range of microbial communities over hundreds of millions of years, this has drastically influenced their adaptation to biotic and abiotic stress. The rapid development of multi-omics approaches has greatly improved our understanding of the diversity, composition, and functions of plant microbiomes, but how global climate change affects the assembly of plant microbiomes and their roles in regulating host plant adaptation to changing environmental conditions is not fully known. In this review, we summarize recent advancements in the community assembly of plant microbiomes, and their responses to climate change factors such as elevated CO2 levels, warming, and drought. We further delineate the research trends and hotspots in plant-microbiome interactions in the context of climate change, and summarize the key mechanisms by which plant microbiomes influence plant adaptation to the changing climate. We propose that future research is urgently needed to unravel the impact of key plant genes and signal molecules modulated by climate change on microbial communities, to elucidate the evolutionary response of plant-microbe interactions at the community level, and to engineer synthetic microbial communities to mitigate the effects of climate change on plant fitness.

Effects of continuous cropping on bacterial community diversity and soil metabolites in soybean roots

The alternating planting of corn and soybeans is regarded as an effective strategy in addressing the challenges faced in soybean cultivation. However, the precise mechanisms that control the bacterial microbiome in soybean roots in the soil, particularly in continuous cropping and rotational corn-soybean farming rotations, are remain unclear. This study employed both field and pot positioning experiments, using high-throughput and generic metabolomics sequencing techniques to explore the dynamics between soybean plants, root microflora, and soil metabolites, especially in the context of continuous cropping and fluctuating corn-soybean crop rotation. The process that included rotating corn soybeans significantly enhanced their grain yield, dry weight, soil nitrogen concentration, urease activity, as well as the accumulation of nitrogen, phosphorus, and potassium in various plant organs, compared to the traditional practice of continuous soybean cultivation. There is a significant reduction in the transit of bacterial operational taxonomic units (OTUs) from the rhizosphere to the endosphere through rhizoplane. The number of bacterial OTUs that are consumed and enriched on rhizoplane is greater than those that are enriched and absorbed in the endosphere. Continuous cropping practices significantly boost Burkholderiales, whereas chloroplast microorganisms significantly improve crop rotation techniques. Soil environmental factors, such as urease and accessible phosphorus, are crucial in establishing the relative prevalence of Rhodanobacter and other bacterial groups. Soil metabolites, such as benzyl alcohol, show a positive correlation with Cyanobacteria, while acidic compounds, such as D-arabinitol, are positively linked with Burkholderiales. This study indicates that the rotation of corn and soybean crops facilitates the growth of soybeans, increases nutrient accumulation in both plants and soil, enhances the presence of beneficial bacteria, and improves soybean yields.

Fungal communities in boreal soils are influenced by land use, agricultural soil management, and depth

Land use and agricultural soil management affect soil fungal communities that ultimately influence soil health. Subsoils harbor nutrient reservoir for plants and can play a significant role in plant growth and soil carbon sequestration. Typically, microbial analyses are restricted to topsoil (0-30 cm) leaving subsoil fungal communities underexplored. To address this knowledge gap, we analyzed fungal communities in the vertical profile of four boreal soil treatments: long-term (24 years) organic and conventional crop rotation, meadow, and forest. Internal transcribed spacer (ITS2) amplicon sequencing revealed soil-layer-specific land use or agricultural soil management effects on fungal communities down to the deepest measured soil layer (40-80 cm). Compared to other treatments, higher proportion of symbiotrophs, saprotrophs, and pathotrophs + plant pathogens were found in forest, meadow and crop rotations, respectively. The proportion of arbuscular mycorrhizal fungi was higher in deeper (>20 cm) soil than in topsoil. Forest soil below 20 cm was dominated by fungal functional groups with proposed interactions with plants or other soil biota, whether symbiotrophic or pathotrophic. Ferrous oxide was an important factor shaping fungal communities throughout the vertical profile of meadow and cropping systems. Our results emphasize the importance of including subsoil in microbial community analyses in differently managed soils.

Effects of cotton peanut rotation on crop yield soil nutrients and microbial diversity

Background and Aims Cotton-peanut rotation is a sustainable farming practice that enhances land utilization and promotes the sustainable development of agriculture. Crop rotation can reduce the occurrence of pests and diseases, as different crops have varying levels of resistance to such threats. Additionally, by alternating the types of crops grown, the soil environment is changed, which can lead to the elimination of favorable conditions for pathogens and pests, thereby alleviating the impact of these issues. Furthermore, cotton-peanut rotation can improve soil fertility.To investigate the effects of different crop rotation systems on crop yield, soil nutrients, and soil microbial communities.

METHODS

Using high-throughput sequencing technology, investigate the soil microbial diversity in the root zone after cotton-peanut rotation.Various planting patterns, including cotton continuous cropping (MC), peanut continuous cropping (HC), peanut-cotton-peanut rotation (HR), and fallow (X), were established to assess variations in crop yield, soil nutrients, and soil microbial diversity.

RESULTS

Significant differences were observed in crop yield, soil nutrients, and soil microbial community structure among different planting patterns. The HR system significantly increased the output compared with the HC and MC systems. Additionally, HR exhibited significantly lower total nitrogen (N) and basic nitrogen (BN) contents than HC and MC, whereas MC showed lower total potassium (K) and available potassium (AK) contents. HR led to a decrease in soil bacterial diversity but an increase in fungal diversity, with Ascomycota and Mortierellomycota being dominant. Various bacteria (Chloroflexi, Bacteroidota, and Actinobacteriota) associated with organic matter degradation and nutrient cycling were found across different planting systems, enhancing material cycling efficiency. Furthermore, Planctomycetota bacteria related to crop nutrient synthesis and Glomeromycota bacteria aiding plant nutrient absorption were significantly higher in the MC system than in the HR or HC systems. Redundancy analysis indicated a significant negative correlation between crop rotation and soil fungal community, whereas Ascomycota exhibited a significant negative correlation with organic matter.

CONCLUSION

Peanut-cotton rotation can mitigate soil nutrient loss, enhance beneficial microorganism diversity, suppress harmful bacterial populations, stabilize ecosystems, and boost crop yield.

Investigating Microbial Diversity in the Endosphere and Rhizoplane of Three Aromatic Rice Landraces: Implications for Biological Nitrogen Fixation

Biological nitrogen fixation (BNF) occurring in the rhizosphere is a sustainable source of nitrogen for plants. BNF in cereal crops can be promoted by inoculation of a single or consortium of associative and endophytic diazotrophs. Creating a successful nitrogen-fixing biofertilizer necessitates the study of the core microbiome of the plant rhizosphere and the functional relationship of the members. This study compares the endosphere and rhizoplane microbial diversity of three aromatic landraces and one high-yielding variety of rice using culture-independent methods. The V3-V4 variable regions of 16S rRNA were used for amplicon sequencing of soil DNA. Patescibacteria, Planctomycetota, and Proteobacteria were the predominant phyla in all four genotypes. Richness (Chao-1 and ACE) and microbial diversity indices (Shannon and Simpson indices) showed that microbial diversity among the genotypes varies subtly at the phylum level. Beta diversity analysis with the phylum identified and comparisons of the microbiome at the genus level revealed a more prominent effect of plant genotype on microbial diversity. Canonical component analysis drew a correlation between microbial diversity in each genotype with the sugar and N content of these landraces. Paraburkholderia was identified as one of the major OTUs among the known nitrogen fixing followed by Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group, Azospirillum, Hebarspirillum, and Azotobacter.

Effects of microbial agent and microbial fertilizer input on soil microbial community structure and diversity in a peanut continuous cropping system

INTRODUCTION

The soil harbors a diverse array of microorganisms, and these are essential components of terrestrial ecosystems. The presence of microorganisms in the soil, particularly in the rhizosphere, is closely linked to plant growth and soil fertility.

OBJECTIVE

The primary objective of this study is to assess the potential advantages of integrating microbial inoculants with compound fertilizer in enhancing peanut yield.

METHODS

We utilized Illumina MiSeq high-throughput sequencing technology to conduct our investigation. The experimental design consists of four treatment groups: compound fertilizers (CF), compound fertilizers supplemented with microbial agents (CF + MA), compound fertilizers supplemented with microbial fertilizers (CF + MF), and compound fertilizers supplemented with both microbial agents and microbial fertilizers (CF + MM).

RESULTS

The experimental results demonstrated a significant increase in peanut yield upon application of CF + MA, CF + MF, and CF + MM treatments. During the blossom stage and pod-setting stage, the soil's catalase, urease, and acid phosphatase activities were significantly increased in the CF + MA, and CF + MM treatments compared to the CF treatment. The application of CF + MA resulted in an increase in bacterial richness in the rhizosphere soil of peanuts, as indicated by the sequencing results. The application of CF + MA, CF + MF, and CF + MM resulted in a reduction of fungal diversity. Proteobacteria, Actinobacteria, and Acidobacteria were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the dominant phyla in the fungal component of the rhizosphere soil microbiome across all experimental treatments.

CONCLUSION

Microbial agents and fertilizers modify the peanut rhizosphere soil's microbial community structure, as per our findings. The abundance of potentially beneficial bacteria (Bradyrhizobium, Rhizobium, and Burkholderia) and fungi (Trichoderma and Cladophialophora) could increase, while pathogenic fungi (Penicillium and Fusarium) decreased, thereby significantly promoting plant growth and yield of peanut.

Large scale exploration reveals rare taxa crucially shape microbial assembly in alkaline lake sediments

Alkaline lakes are extreme environments inhabited by diverse microbial extremophiles. However, large-scale distribution patterns, environmental adaptations, community assembly, and evolutionary dynamics of microbial communities remain largely underexplored. This study investigated the characteristics of microbial communities on rare and abundant taxa in alkaline lake sediments in west and northwest China. We observed that abundant taxa varied significantly with geographical distance, while rare taxa remained unaffected by regional differences. The assembly process of abundant taxa was influenced by dispersal limitation, whilst rare taxa were predominantly driven by heterogeneous selection. Network analysis indicated that rare taxa as core species for community interactions and community stability. Rare taxa exhibited higher speciation and transition rate than abundant taxa, serving as a genetic reservoir and potential candidates to become abundance taxa, highlighting their crucial role in maintaining microbial diversity. These insights underscore the significant influence of rare taxa on ecosystem biodiversity and stability in alkaline lakes.

Carbon Nanodot-Microbe-Plant Nexus in Agroecosystem and Antimicrobial Applications

The intensive applications of nanomaterials in the agroecosystem led to the creation of several environmental problems. More efforts are needed to discover new insights in the nanomaterial-microbe-plant nexus. This relationship has several dimensions, which may include the transport of nanomaterials to different plant organs, the nanotoxicity to soil microbes and plants, and different possible regulations. This review focuses on the challenges and prospects of the nanomaterial-microbe-plant nexus under agroecosystem conditions. The previous nano-forms were selected in this study because of the rare, published articles on such nanomaterials. Under the study's nexus, more insights on the carbon nanodot-microbe-plant nexus were discussed along with the role of the new frontier in nano-tellurium-microbe nexus. Transport of nanomaterials to different plant organs under possible applications, and translocation of these nanoparticles besides their expected nanotoxicity to soil microbes will be also reported in the current study. Nanotoxicity to soil microbes and plants was investigated by taking account of morpho-physiological, molecular, and biochemical concerns. This study highlights the regulations of nanotoxicity with a focus on risk and challenges at the ecological level and their risks to human health, along with the scientific and organizational levels. This study opens many windows in such studies nexus which are needed in the near future.

Spent Mushroom Substrate Improves Microbial Quantities and Enzymatic Activity in Soils of Different Farming Systems

Organic fertilizers, such as spent mushroom substrate (SMS), improve soil fertility, but studies comparing their effects on different agricultural soils are limited. In this study, the effects of standard, SMS and composed fertilizers on soils from conventional-integrated, organic and biodynamic farming were investigated. Soil samples were analyzed for microorganisms and the activity of β-glucosidase (β-GLU), β-1,4-N-acetylglucosaminidase (NAG), urease (URE), arylamidase (ARN), phosphatase (PHOS), acid phosphatase (PAC), alkaline phosphatase (PAH) and arylsulphatase (ARS). Biodynamic soil showed the highest microbial counts and enzyme activities, followed by organic and conventional soils. SMS significantly increased the number of microorganisms and enzyme activities, especially in biodynamic and organic soils. Seasonal variations affected all microorganisms and most enzymes in all soils, except NAG in conventional and organic soils. Biodynamic soil showed stable activity of enzymes and microorganisms throughout the year, indicating greater stability. This study concludes that soil microorganisms and enzyme activities respond differently to fertilization depending on the soil type, with SMS demonstrating beneficial effects in all tested soils.

Additional organic and bacterium fertilizer input regulated soybean root architecture and dry matter distribution for a sustainable yield in the semi-arid Region of China

In the dryland area of the Loess Plateau in northwest China, long-term excessive fertilization has led to soil compaction and nutrient loss, which in turn limits crop yield and soil productivity. To address this issue, we conducted experiments using environmentally friendly organic fertilizer and bacterium fertilizer. Our goal was to investigate the effects of additional organic and bacterium fertilizer inputs on soil water migration, crop root architecture, and yield formation. We implemented six different fertilizer strategies, namely: Nm (mulching, N 30 kg/ha), NPK1m (mulching, N 60 kg/ha; P 30 kg/ha; K 30 kg/ha), NPK2m (mulching, N 90 kg/ha; P 45 kg/ha; K 30 kg/ha), NPKOm (mulching, N 90 kg/ha; P 45 kg/ha; K 30 kg/ha; organic fertilizer 2 t/ha), NPKBm (mulching, N 60 kg/ha; P 30 kg/ha; K 30 kg/ha; bacterium fertilizer 10 kg/ha), and N (N 30 kg/ha; no mulching). The results revealed that the addition of bacterium fertilizer (NPKBm) had a positive impact on soybean root system development. Compared with the other treatments, it significantly increased the total root length, total root surface area, and total root length density by 25.96% ~ 94.89%, -19.63% ~ 36.28%, and 9.36% ~ 28.84%, respectively. Furthermore, NPKBm enhanced soil water consumption. In 2018, water storage during the flowering and podding periods decreased by 12.63% and 19.65%, respectively, while water consumption increased by 0.97% compared to Nm. In 2019, the flowering and harvest periods decreased by 23.49% and 11.51%, respectively, while water consumption increased by 0.65%. Ultimately, NPKBm achieved high grain yield and significantly increased water use efficiency (WUE), surpassing other treatments by 76.79% ~ 78.97% and 71.22% ~ 73.76%, respectively. Subsequently, NPK1m also exhibited significant increases in yield and WUE, with improvements of 35.58% ~ 39.27% and 35.26% ~ 38.16%, respectively. The use of bacterium fertilizer has a profound impact on soybean root architecture, leading to stable and sustainable grain yield production.

Soil fungal community structure and function response to rhizoma perennial peanut cultivars

BACKGROUND

Crop-associated microorganisms play a crucial role in soil nutrient cycling, and crop growth, and health. Fine-scale patterns in soil microbial community diversity and composition are commonly regulated by plant species or genotype. Despite extensive reports in different crop or its cultivar effects on the microbial community, it is uncertain how rhizoma peanut (RP, Arachis glabrata Benth.), a perennial warm-season legume forage that is well-adapted in the southern USA, affects soil microbial community across different cultivars.

RESULTS

This study explored the influence of seven different RP cultivars on the taxonomic composition, diversity, and functional groups of soil fungal communities through a field trial in Marianna, Florida, Southern USA, using next-generation sequencing technique. Our results showed that the taxonomic diversity and composition of the fungal community differed significantly across RP cultivars. Alpha diversity (Shannon, Simpson, and Pielou's evenness) was significantly higher in Ecoturf but lower in UF_Peace and Florigraze compared to other cultivars (p < 0.001). Phylogenetic diversity (Faith's PD) was lowest in Latitude compared to other cultivars (p < 0.0001). The dominant phyla were Ascomycota (13.34%), Mortierellomycota (3.82%), and Basidiomycota (2.99%), which were significantly greater in Florigraze, UF_Peace, and Ecoturf, respectively. The relative abundance of Neocosmospora was markedly high (21.45%) in UF_Tito and showed large variations across cultivars. The relative abundance of the dominant genera was significantly greater in Arbrook than in other cultivars. There were also significant differences in the co-occurrence network, showing different keystone taxa and more positive correlations than the negative correlations across cultivars. FUNGuild analysis showed that the relative abundance of functional guilds including pathogenic, saprotrophic, endophytic, mycorrhizal and parasitic fungi significantly differed among cultivars. Ecoturf had the greatest relative abundance of mycorrhizal fungal group (5.10 ± 0.44), whereas UF_Peace had the greatest relative abundance of endophytic (4.52 ± 0.56) and parasitic fungi (1.67 ± 0.30) compared to other cultivars.

CONCLUSIONS

Our findings provide evidence of crop cultivar's effect in shaping fine-scale fungal community patterns in legume-based forage systems.

Spatial distribution and community composition of endophytic fungi within Mussaenda pubescens stems

Endophytic fungi, pivotal in facilitating plant co-evolution, significantly enhance plant growth, stress resistance, and environmental adaptability. Despite their importance, the spatial distribution of stem endophytic fungi (SEF) within host plants remains poorly characterized. Here, we employed high-throughput sequencing to conduct a comparative analysis of SEF communities in Mussaenda pubescens on a regional scale. Our findings reveal that whole-SEF communities were overwhelmingly dominated by members of the phylum Ascomycota, accounting for 85.9 %, followed by Basidiomycota at 13.9 %, and that alpha diversity within the whole-SEF community of M. pubescens remains relatively consistent across sampling sites. However, significant variation was observed within conditionally abundant taxa (CAT), conditionally rare or abundant taxa (CRAT), and conditionally rare taxa (CRT). Climatic factors emerged as the primary influence on SEF community distribution, followed by spatial distance and stem chemical properties. Neutral community modeling results suggested that both stochastic and deterministic processes play a role in shaping whole-SEF communities, with deterministic processes having a stronger influence on CRT subcommunities. Furthermore, the CRT co-occurrence network exhibited a more complex structure, characterized by higher values of network betweenness and degree relative to CAT and CRAT subcommunities. These findings enhance our understanding of community assembly and ecological interactions between stem fungal endophytes, presenting opportunities for harnessing fungal resources for the benefit of humanity.

Effects of Rice-Frog Co-Cropping on the Soil Microbial Community Structure in Reclaimed Paddy Fields

Utilizing and improving the productivity of reclaimed land are highly significant for alleviating the problem of food production shortage in China, and the integrated rice-frog farming model can improve soil fertility. However, there are few studies on the use of integrated rice-frog farming technology to improve the fertility of reclaimed land and increase its efficiency in food production. Therefore, this study was conducted to evaluate the effects of the rice-frog co-cropping mode on the soil fertility and microbial diversity of reclaimed land. A rice monoculture group (SF), low-density rice-frog co-cropping group (SD, 5000 frogs/mu, corresponds to 8 frogs/m2), and high-density rice-frog co-cropping group (SG, 10,000 frogs/mu, corresponds to 15 frogs/m2) were established and tested. The contents of total nitrogen, soil organic matter, available potassium, and available phosphorus of the soil in the SG group were significantly higher than those in the SF group (p < 0.05) in the mature stage of rice. Compared with the SF group, the SD and SG groups improved the soil microbial diversity and changed the structure of the microbial community. This study indicates that compared with the rice monoculture mode, the rice-frog co-cropping pattern can improve the soil fertility, as well as microbial diversity, of reclaimed land.

Who inhabits the built environment? A microbiological point of view on the principal bacteria colonizing our urban areas

Modern lifestyle greatly influences human well-being. Indeed, nowadays people are centered in the cities and this trend is growing with the ever-increasing population. The main habitat for modern humans is defined as the built environment (BE). The modulation of life quality in the BE is primarily mediated by a biodiversity of microbes. They derive from different sources, such as soil, water, air, pets, and humans. Humans are the main source and vector of bacterial diversity in the BE leaving a characteristic microbial fingerprint on the surfaces and spaces. This review, focusing on articles published from the early 2000s, delves into bacterial populations present in indoor and outdoor urban environments, exploring the characteristics of primary bacterial niches in the BE and their native habitats. It elucidates bacterial interconnections within this context and among themselves, shedding light on pathways for adaptation and survival across diverse environmental conditions. Given the limitations of culture-based methods, emphasis is placed on culture-independent approaches, particularly high-throughput techniques to elucidate the genetic and -omic features of BE bacteria. By elucidating these microbiota profiles, the review aims to contribute to understanding the implications for human health and the assessment of urban environmental quality in modern cities.

The Contributions of Sub-Communities to the Assembly Process and Ecological Mechanisms of Bacterial Communities along the Cotton Soil-Root Continuum Niche Gradient

Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil-root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil-root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root-soil continuum.

A comparative analysis of soil physicochemical properties and microbial community structure among four shelterbelt species in the northeast China plain

Conducting studies that focus on the alterations occurring in the soil microbiome within protection forests in the northeast plain is of utmost importance in evaluating the ecological rehabilitation of agricultural lands in the Mollisols region. Nevertheless, the presence of geographic factors contributes to substantial disparities in the microbiomes, and thus, addressing this aspect of influence becomes pivotal in ensuring the credibility of the collected data. Consequently, the objective is to compare the variations in soil physicochemical properties and microbial community structure within the understory of diverse shelterbelt species. In this study, we analyzed the understory soils of Juglans mandshurica (Jm), Fraxinus mandschurica (Fm), Acer mono (Am), and Betula platyphylla (Bp) from the same locality. We employed high-throughput sequencing technology and soil physicochemical data to investigate the impact of these different tree species on soil microbial communities, chemical properties, and enzyme activities in Mollisols areas. Significant variations in soil nutrients and enzyme activities were observed among tree species, with soil organic matter content ranging from 49.1 to 67.7 g/kg and cellulase content ranging from 5.3 to 524.0 μg/d/g. The impact of tree species on microbial diversities was found to be more pronounced in the bacterial community (Adnoism: R = 0.605) compared to the fungal community (Adnoism: R = 0.433). The linear discriminant analysis effect size (LEfSe) analysis revealed a total of 5 (Jm), 3 (Bp), and 6 (Am) bacterial biomarkers, as well as 2 (Jm), 6 (Fm), 4 (Bp), and 1 (Am) fungal biomarker at the genus level (LDA3). The presence of various tree species was observed to significantly alter the relative abundance of specific microbial community structures, specifically in Gammaproteobacteria, Ascomycota, and Basidiomycota. Furthermore, environmental factors, such as pH, total potassium, and available phosphorus were important factors influencing changes in bacterial communities. We propose that Fm be utilized as the primary tree species for establishing farmland protection forests in the northeastern region, owing to its superior impact on enhancing soil quality.

IMPORTANCE

The focal point of this study lies in the implementation of a controlled experiment conducted under field conditions. In this experiment, we deliberately selected four shelterbelts within the same field, characterized by identical planting density, and planting year. This deliberate selection effectively mitigated the potential impact of extraneous factors on the three microbiomes, thereby enhancing the reliability and validity of our findings.

Chiral herbicide imazethapy influences plant-soil feedback on nitrogen metabolism by shaping rhizosphere microorganisms

Herbicides are known to affect the soil nitrogen cycle by shaping soil microorganisms. However, it is not clear how herbicides regulate diverse transformation processes of soil nitrogen cycling by altering rhizosphere microorganisms, subsequently influencing the feedback to plant nitrogen metabolism. Here, we investigated how imazethapyr (IM) enantiomers drive plant-soil feedback on nitrogen metabolism by altering the rhizosphere microorganisms. The results indicated that (R)- and (S)-IM significantly changed the composition and structure rhizosphere microbiome with enantioselectivity and functional changes in microbial communities were associated with soil nitrogen circulation. The determination of nitrogen-cycling functional genes further supported the above findings. The results revealed that (R)- and (S)-IM could change the abundance of nitrogen-cycling functional genes by changing specific bacteria abundances, such as Bacteroidetes, Proteobacteria, and Acidobacteria, thus resulting in diverse nitrogen transformation processes. The alternation of nitrogen transformation processes indicated (R)-IM exhibited a more notable tendency to form a nitrogen cycling pattern with lower energy cost and higher nitrogen retention than (S)-IM. Sterilization experiments demonstrated changes in soil nitrogen cycling drive plant nitrogen metabolism and rhizosphere microorganisms are responsible for the above process of plant-soil feedback for nitrogen metabolism. Under IM enantiomer treatments, rhizosphere microorganisms might stimulate glutamate synthesis by promoting NH4+ uptake and glutamine-glutamate synthesis cycling in roots, thus contributing to positive feedback, with (R)-IM treatments showing more pronounced positive feedback on nitrogen metabolism than (S)-IM treatments. Our results provide theoretical support for determining the mechanism by which IM enantiomers drive plant-soil nitrogen metabolism by changing the rhizosphere microbial communities.

Traditional potato tillage systems in the Peruvian Andes impact bacterial diversity, evenness, community composition, and functions in soil microbiomes

The soil microbiome, a crucial component of agricultural ecosystems, plays a pivotal role in crop production and ecosystem functioning. However, its response to traditional tillage systems in potato cultivation in the Peruvian highlands is still far from understood. Here, ecological and functional aspects of the bacterial community were analyzed based on soil samples from two traditional tillage systems: 'chiwa' (minimal tillage) and 'barbecho' (full tillage), in the Huanuco region of the Peruvian central Andes. Similar soil bacterial community composition was shown for minimal tillage system, but it was heterogeneous for full tillage system. This soil bacterial community composition under full tillage system may be attributed to stochastic, and a more dynamic environment within this tillage system. 'Chiwa' and 'barbecho' soils harbored distinct bacterial genera into their communities, indicating their potential as bioindicators of traditional tillage effects. Functional analysis revealed common metabolic pathways in both tillage systems, with differences in anaerobic pathways in 'chiwa' and more diverse pathways in 'barbecho'. These findings open the possibilities to explore microbial bioindicators for minimal and full tillage systems, which are in relationship with healthy soil, and they can be used to propose adequate tillage systems for the sowing of potatoes in Peru.

Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil

The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.

Beyond compliance: harmonising research and husbandry practices to improve experimental reproducibility using fish models

Reproducibility in animal research is impacted by the environment, by husbandry practices in the laboratory and by the animals' provenance. These factors, however, are often not adequately considered by researchers. A disconnect between researchers and animal care staff can result in inappropriate housing and husbandry decisions for scientific studies with those animals. This is especially the case for the research in neuro-behaviour, epigenetics, and the impact of climate change, as heritable phenotypic, behavioural or physiological changes are known to result from the animals' environmental housing, husbandry, provenance and prior experience. This can lead to greater variation (even major differences) in data outcomes among studies, driving scientific uncertainties. Herein, we illustrate some of the endpoints measured in fish studies known to be intrinsically linked to the environment and husbandry conditions and assess the significance of housing and husbandry practice decisions for research adopting these endpoints for different fish species. We highlight the different priorities and challenges faced by researchers and animal care staff and how harmonising their activities and building greater understanding of how husbandry practices affect the fish will improve reproducibility in research outcomes. We furthermore illustrate how improving engagement between stakeholders, including regulatory bodies, can better underpin fish husbandry decisions and where researchers could help to drive best husbandry practices through their own research with fish models.

The mechanism of microbial community succession and microbial co-occurrence network in soil with compost application

The application of organic and chemical fertilizer into soil can regulate microbial communities. However, the response mechanism of microbial communities in soil to compost and chemical fertilizer application remain unclear. In this study, compost made of tobacco leaves individually and combined with chemical fertilizer was applied, respectively, to investigate their effect on soil microorganisms during the pot-culture process. High-throughput sequence, neutral community model and null model were employed to clarify how soil microbial community respond to the application of compost and chemical fertilizer. Furthermore, random forest model was applied to predict the relationships between the plant agronomical traits and the soil microorganism during the pot-culture process. The results demonstrated that the simultaneous application of compost and chemical fertilizer increased significantly the richness and diversity of the microorganisms in soil (p < 0.05), groups C and D led to a significant reduction in the number of nodes and edges in the microbial network (77.78 %-96.57 %). The dominant bacteria in the application of 50 g fertilizer accounted for the highest proportion (40 %) and organic matter was the main factors driving the change in bacterial communities. Compared to the tilled soil, the microbial communities of the soil with the simultaneous application of compost and chemical fertilizer were more susceptible to stochastic processes, and soil microorganisms had less influence on the growth of crops during pot-culture. In conclusion, the simultaneous application of compost and fertilizer altered the ecological functions of soil microbial communities, leading to an enhanced stochastic process of community formation.

Attribution of dispersal limitation can better explain the assembly patterns of plant microbiota

Disentangling community assembly processes is crucial for fully understanding the function of microbiota in agricultural ecosystems. However, numerous plant microbiome surveys have gradually revealed that stochastic processes dominate the assembly of the endophytic root microbiota in conflict with strong host filtering effects, which is an important issue. Resolving such conflicts or inconsistencies will not only help accurately predict the composition and structure of the root endophytic microbiota and its driving mechanisms, but also provide important guidance on the correlation between the relative importance of deterministic and stochastic processes in the assembly of the root endophytic microbiota, and crop productivity and nutritional quality. Here, we propose that the inappropriate division of dispersal limitation may be the main reason for such inconsistency, which can be resolved after the proportion of dispersal limitation is incorporated into the deterministic processes. The rationality of this adjustment under the framework of the formation of a holobiont between the microbiome and the plant host is herein explained, and a potential theoretical framework for dynamic assembly patterns of endophytic microbiota along the soil-plant continuum is proposed. Considering that the assembly of root endophytic microbiota is complicated, we suggest caution and level-by-level verification from deterministic processes to neutral components to stochastic processes when deciding on the attribution of dispersal limitation in the future to promote the expansion and application of microbiome engineering in sustainable agricultural development based on community assembly patterns.

From salty to thriving: plant growth promoting bacteria as nature's allies in overcoming salinity stress in plants

Soil salinity is one of the main problems that affects global crop yield. Researchers have attempted to alleviate the effects of salt stress on plant growth using a variety of approaches, including genetic modification of salt-tolerant plants, screening the higher salt-tolerant genotypes, and the inoculation of beneficial plant microbiome, such as plant growth-promoting bacteria (PGPB). PGPB mainly exists in the rhizosphere soil, plant tissues and on the surfaces of leaves or stems, and can promote plant growth and increase plant tolerance to abiotic stress. Many halophytes recruit salt-resistant microorganisms, and therefore endophytic bacteria isolated from halophytes can help enhance plant stress responses. Beneficial plant-microbe interactions are widespread in nature, and microbial communities provide an opportunity to understand these beneficial interactions. In this study, we provide a brief overview of the current state of plant microbiomes and give particular emphasis on its influence factors and discuss various mechanisms used by PGPB in alleviating salt stress for plants. Then, we also describe the relationship between bacterial Type VI secretion system and plant growth promotion.

Potential effect of key soil bacterial taxa on the increase of rice yield under milk vetch rotation

Legume crop rotation is often adopted in rice cultivation to improve soil productivity. However, little is known about the role of microbes under legume rotation in affecting soil productivity. To elucidate this, a long-term paddy cropping experiment was set up to study the relationship between crop yield, soil chemical properties, and key microbial taxa under a double-rice and milk vetch rotation. Milk vetch rotation significantly improved soil chemical properties compared to no fertilization treatment, and soil phosphorus was a major factor correlated with crop yield. Long-term legume rotation increased soil bacterial alpha diversity and changed soil bacterial community. After milk vetch rotation, the relative abundances of Bacteroidota, Desulfobacterota, Firmicutes, and Proteobacteria increased while those of Acidobacteriota, Chloroflexi, and Planctomycetota decreased. Moreover, milk vetch rotation increased the relative abundance of phosphorus-related gene K01083 (bpp), which was significantly correlated with soil phosphorus content and crop yield. Network analysis showed that taxa of Vicinamibacterales were positively correlated with total phosphorus and available phosphorus, which was a potential taxon contributing to the availability of soil phosphorus stock. Our results indicated that milk vetch rotation could enrich key taxa with latent phosphate-solubilizing ability, increase the content of soil available phosphorus, and finally enhance crop yield. This could provide scientific guidance for better crop production.

Microbial community assembly of the hyperaccumulator plant Sedum plumbizincicola in two contrasting soil types with three levels of cadmium contamination

Microbial communities are closely related to plant performance and numerous studies have shown their involvement with the growth and development of host plants, resistance to pathogen invasion and adaptation to environmental stress. Here we described in detail the ecological process of the microbial community assembly in hyperaccumulator plant Sedum plumbizincicola. We divided the microbiota into four ecological compartments (bulk soil, rhizosphere, root endosphere and aboveground endosphere). The results showed that host selection strongly controlled the aggregation of microbial community. So that microbes occupied different niches from the bulk soil to the aboveground endosphere, and bacterial diversity and network complexity decreased gradually. Soil types were the second influencing factor, especially for the microbial community in the root endosphere. The SourceTracker analysis further confirmed the vertical migration of microbes from bulk soil to aboveground endosphere. In addition, under the condition of heavy metal pollution, the microbial community of S. plumbizincicola tended to form a microbial pool dominated by Proteobacteria and Actinobacteria. Ellin6067, Sphingomonas, Ralstonia, SC-I-84_uncultured bacterium, Burkholderiaceae_Undibacterium and Pedosphaeraceae_uncultured bacterium etc. were identified as the vital biomarker taxa. Among these genera, the relative abundance of last three was significantly positively correlated with the activation and transfer of cadmium, and they mainly enriched in paddy soil. This study provides evidence for the mechanism by which the microbial community assembly occurs and experience for regulating the microbial community and increasing the accumulation efficiency of potentially toxic metals in S. plumbizincicola.

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites

Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha^-1 , LN) and high N (180 kg N ha^-1 , HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N₂ O emission and high rhizosphere NO₃ ^- -N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.

Soil Microbial Community Responses to Different Management Strategies in Almond Crop

A comparative study of organic and conventional farming systems was conducted in almond orchards to determine the effect of management practices on their fungal and bacterial communities. Soils from two orchards under organic (OM) and conventional (CM), and nearby nonmanaged (NM) soil were analyzed and compared. Several biochemical and biological parameters were measured (soil pH, electrical conductivity, total nitrogen, organic material, total phosphorous, total DNA, and fungal and bacterial DNA copies). Massive parallel sequencing of regions from fungal ITS rRNA and bacterial 16 S genes was carried out to characterize their diversity in the soil. We report a larger abundance of bacteria and fungi in soils under OM, with a more balanced fungi:bacteria ratio, compared to bacteria-skewed proportions under CM and NM. The fungal phylum Ascomycota corresponded to around the 75% relative abundance in the soil, whereas for bacteria, the phyla Proteobacteria, Acidobacteriota and Bacteroidota integrated around 50% of their diversity. Alpha diversity was similar across practices, but beta diversity was highly clustered by soil management. Linear discriminant analysis effect size (LEfSE) identified bacterial and fungal taxa associated with each type of soil management. Analyses of fungal functional guilds revealed 3-4 times larger abundance of pathogenic fungi under CM compared to OM and NM treatments. Among them, the genus Cylindrocarpon was more abundant under CM, and Fusarium under OM.

Structural characteristics and diversity of the rhizosphere bacterial communities of wild Fritillaria przewalskii Maxim. in the northeastern Tibetan Plateau

Introduction

Fritillaria przewalskii Maxim. is a Chinese endemic species with high medicinal value distributed in the northeastern part of the Tibetan Plateau. F. przewalskii root-associated rhizosphere bacterial communities shaped by soil properties may maintain the stability of soil structure and regulate F. przewalskii growth, but the rhizosphere bacterial community structure of wild F. przewalskii from natural populations is not clear.

Methods

In the current study, soil samples from 12 sites within the natural range of wild F. przewalskii were collected to investigate the compositions of bacterial communities via high-throughput sequencing of 16S rRNA genes and multivariate statistical analysis combined with soil properties and plant phenotypic characteristics.

Results

Bacterial communities varied between rhizosphere and bulk soil, and also between sites. Co-occurrence networks were more complex in rhizosphere soil (1,169 edges) than in bulk soil (676 edges). There were differences in bacterial communities between regions, including diversity and composition. Proteobacteria (26.47-37.61%), Bacteroidetes (10.53-25.22%), and Acidobacteria (10.45-23.54%) were the dominant bacteria, and all are associated with nutrient cycling. In multivariate statistical analysis, both soil properties and plant phenotypic characteristics were significantly associated with the bacterial community (p < 0.05). Soil physicochemical properties accounted for most community differences, and pH was a key factor (p < 0.01). Interestingly, when the rhizosphere soil environment remained alkaline, the C and N contents were lowest, as was the biomass of the medicinal part bulb. This might relate to the specific distribution of genera, such as Pseudonocardia, Ohtaekwangia, Flavobacterium (relative abundance >0.01), which all have significantly correlated with the biomass of F. przewalskii (p < 0.05).

Discussion

F. przewalskii is evidently averse to alkaline soil with high potassium contents, but this requires future verification. The results of the present study may provide theoretical guidance and new insights for the cultivation and domestication of F. przewalskii.

Periphytic biofilms function as a double-edged sword influencing nitrogen cycling in paddy fields

It remains unclear whether periphytic biofilms are beneficial to N cycling in paddy fields. Here, based on a national-scale field investigation covering 220 rice fields in China, the N accumulation potential of periphytic biofilms was found to decrease from 8.8 ± 2.4 to 4.5 ± 0.7 g/kg and 3.1 ± 0.6 g/kg with increasing habitat latitude and longitude, respectively. The difference in abundant and rare subcommunities likely accounts for their geo-difference in N accumulation potential. The N cycling pathways involved in periphytic biofilms inferred that soil N and N₂ were two potential sources for N accumulation in periphytic biofilms. Meanwhile, some of the accumulated N may be lost via N₂ , N₂ O, NO, or NH₃ outputs. Superficially, periphytic biofilms are double-edged swords to N cycling by increasing soil N through biological N fixation but accelerating greenhouse gas emissions. Essentially, augmented periphytic biofilms increased change of TN (ΔTN) content in paddy soil from -231.9 to 31.9 mg/kg, indicating that periphytic biofilms overall benefit N content enhancement in paddy fields. This study highlights the contribution of periphytic biofilms to N cycling in rice fields, thus, drawing attention to their effect on rice production and environmental security.