Anthropogenic drivers of soil microbial communities and impacts on soil biological functions in agroecosystems

Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil

Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.

Environmental determinants of spatial-temporal variability in ammonia oxidizing microorganisms across diverse Chinese agricultural soils

Numerous studies investigated the variation of soil ammonia oxidizing microorganisms along the geographic distance, but few highlighted the associated influence of agricultural practices on ammonia oxidizing communities and functions. To make up this gap, we determined the variation of ammonia-oxidizing archaea (AOA), bacteria (AOB), and soil nitrification within eight typical agricultural plots across China. The current study revealed significant variations in soil potential nitrification rates (PNRs) and the diversity and composition of AOA and AOB communities across various plots. Spearman correlation analysis revealed a significant link between soil PNRs and alpha diversity, specific AOA and AOB taxa, but no significant correlation was found with amoA gene abundance. Structural equation modeling and canonical correspondence analysis showed that factors like MAT, clay content, CEC, and soil carbon and nitrogen levels significantly influenced the diversity and composition of AOA. In contrast, AOB were more significantly impacted by soil pH and carbon- and nitrogen-related nutrients, but less associated with MAP and soil clay content. Notably, soil PNRs were found to be closely linked to AOB diversity, soil pH, and ammonium nitrogen (NH4N) levels. This research highlights the contributing role of AOB group in soil nitrification and the related driving factors from agricultural practices.

Rhizosphere-associated bacterial and fungal communities of two maize hybrids under increased nitrogen fertilization

Introduction

The selection and application of nitrogen-efficient maize hybrids have significantly bolstered contemporary food security. Nevertheless, the effects of heightened nitrogen fertilizer demand of these crops on the composition and assembly of soil microbial communities in agricultural production require further elucidation.

Methods

In this study, the effects of four nitrogen fertilizer managements on rhizosphere bacterial and fungal community assembly, co-occurrence network and function of two maize hybrids (LD981 and DH605) were compared.

Results and discussion

Findings revealed that the bacterial community was primarily shaped by deterministic processes, while stochastic processes played a pivotal role in fungal community assembly. N-efficient hybrid DH605 had a more stable microbial network than N-inefficient hybrid LD981. At N3 (130 g N/m2) rate, the bacterial and fungal community networks were the most complex but unstable, followed by N2 (87 g N/m2), N0 (0 g N/m2), and N1 (43 g N/m2) rates. Excessive nitrogen rate (N3) increased the relative abundance of denitrification genes nirK and norB by enriching nitrogen-related genus such as Nitrolancea and Nitrosospira. It led to an increase in the relative abundance of pathways such as cysteine and methionine metabolism and pyruvate metabolism. The effects of management practices (i.e. maize hybrids and N rates) on microbial communities were ultimately directly or indirectly reflected in microbial functions. Our findings illustrate the relationship between the appropriate selection of crop hybrids and management measures in optimizing rhizosphere microbial community assembly and promoting nitrogen use, which is necessary for sustainable food security.

Effects of the tobacco-maize relay intercropping pattern on soil nutrients and soil microbial diversity

The imbalanced soil nutrient status caused by the long-term monoculture of flue-cured tobacco are a concern. The tobacco-maize relay intercropping, widely used in Yunnan, may improve soil nutrients by enhancing the soil microbial community, but this remains unexplored. This study employed high-throughput sequencing technology to examine soil microbial diversity under tobacco monoculture and tobacco-maize relay intercropping, using the varieties Hongda and K326, respectively. The results indicated that tobacco-maize relay intercropping significantly enhanced root biomass compared to tobacco monoculture, with no significant effect on aboveground biomass. This intercropping treatment also significantly improved soil physicochemical properties, including soil pH, total phosphorus, available phosphorus, and available potassium, which was associated with an increase in the soil microbial community (as indicated by the Chao1 and Shannon indices). Specifically, the abundance of arbuscular mycorrhizal fungi, Nitrospira, and Acidobacteria increased, but the abundance of Chloroflexi decreased. Therefore, these findings suggest that tobacco-maize relay intercropping can improve soil physicochemical properties and enhance soil nutrient supply.

Anthropogenic fertilization influences a shift in barley rhizosphere microbial communities

Background

Anthropogenic mediations contribute a significant role in stimulating positive reactions in soil-plant interactions; however, methodical reports on how anthropogenic activities impact soil microorganism-induced properties and soil health are still inadequate. In this study, we evaluated the influence of anthropogenic fertilization of farmland soil on barley rhizosphere microbial community structure and diversity, and the significant impacts on agro-ecosystem productivity. This will help validate the premise that soil amendment with prolonged synthetic fertilizers can lead to a significant reduction in bacterial abundance and diversity, while soils amended with organic fertilizers elicit the succession of the native soil microbial community and favor the growth of copiotrophic bacteria.

Methods

The total metagenomic DNA was extracted from soils obtained from the barley rhizosphere under chemical fertilization (CB), organic fertilization (OB), and bulk soil (NB). Subsequently, these samples were sequenced using an amplicon-based sequencing approach, and the raw sequence dataset was examined using a metagenomic rast server (MG-RAST).

Results

Our findings showed that all environments (CB, OB, and NB) shared numerous soil bacterial phyla but with different compositions. However, Bacteroidetes, Proteobacteria, and Actinobacteria predominated in the barley rhizosphere under chemical fertilization, organic fertilization, and bulk soils, respectively. Alpha and beta diversity analysis showed that the diversity of bacteria under organic barley rhizosphere was significantly higher and more evenly distributed than bacteria under chemical fertilization and bulk soil.

Conclusion

Understanding the impact of conventional and organic fertilizers on the structure, composition, and diversity of the rhizosphere microbiome will assist in soil engineering to enhance microbial diversity in the agroecosystem.

Drivers and human impacts on topsoil bacterial and fungal community biogeography across Australia

Soil microbial diversity mediates a wide range of key processes and ecosystem services influencing planetary health. Our knowledge of microbial biogeography patterns, spatial drivers and human impacts at the continental scale remains limited. Here, we reveal the drivers of bacterial and fungal community distribution in Australian topsoils using 1384 soil samples from diverse bioregions. Our findings highlight that climate factors, particularly precipitation and temperature, along with soil properties, are the primary drivers of topsoil microbial biogeography. Using random forest machine-learning models, we generated high-resolution maps of soil bacteria and fungi across continental Australia. The maps revealed microbial hotspots, for example, the eastern coast, southeastern coast, and west coast were dominated by Proteobacteria and Acidobacteria. Fungal distribution is strongly influenced by precipitation, with Ascomycota dominating the central region. This study also demonstrated the impact of human modification on the underground microbial community at the continental scale, which significantly increased the relative abundance of Proteobacteria and Ascomycota, but decreased Chloroflexi and Basidiomycota. The variations in microbial phyla could be attributed to distinct responses to altered environmental factors after human modifications. This study provides insights into the biogeography of soil microbiota, valuable for regional soil biodiversity assessments and monitoring microbial responses to global changes.

Effects of Vineyard Agro-management Practices on Soil Bacterial Community Composition, and Diversity

Changes in land use strongly affect soil biological and physico-chemical structure and characteristics, which are strongly related to agricultural conversion of natural habitats to man-made usage. These are among the most important and not always beneficial changes, affecting loss of habitats. In Golan Heights basaltic soils, vineyards are currently a driving force in land-use change. Such changes could have an important effect on soil microbial community that play an important role in maintaining stable functioning of soil ecosystems. This study investigated the microbial communities in five different agro-managements using molecular tools that can clarify the differences in microbial community structure and function. Significant differences in soil microbial community composition were found. However, no differences in alpha diversity or functionality were found between the treatments. To the best of our knowledge, this is the first report indicating that the bacterial community in different agro-managements provide an insight into the potential function of a vineyard system.

Microbial Catabolic Activity: Methods, Pertinence, and Potential Interest for Improving Microbial Inoculant Efficiency

Microbial catabolic activity (MCA) defined as the degrading activity of microorganisms toward various organic compounds for their growth and energy is commonly used to assess soil microbial function potential. For its measure, several methods are available including multi-substrate-induced respiration (MSIR) measurement which allow to estimate functional diversity using selected carbon substrates targeting specific biochemical pathways. In this review, the techniques used to measure soil MCA are described and compared with respect to their accuracy and practical use. Particularly the efficiency of MSIR-based approaches as soil microbial function indicators was discussed by (i) showing their sensitivity to different agricultural practices including tillage, amendments, and cropping systems and (ii) by investigating their relationship with soil enzyme activities and some soil chemical properties (pH, soil organic carbon, cation exchange capacity). We highlighted the potential of these MSIR-based MCA measurements to improve microbial inoculant composition and to determine their potential effects on soil microbial functions. Finally, we have proposed ideas for improving MCA measurement notably through the use of molecular tools and stable isotope probing which can be combined with classic MSIR methods. Graphical abstract describing the interrelation between the different parts and the concepts developed in the review.

Effects of Long-Term (17 Years) Nitrogen Input on Soil Bacterial Community in Sanjiang Plain: The Largest Marsh Wetland in China

Increased nitrogen (N) input from natural factors and human activities may negatively impact the health of marsh wetlands. However, the understanding of how exogenous N affects the ecosystem remains limited. We selected the soil bacterial community as the index of ecosystem health and performed a long-term N input experiment, including four N levels of 0, 6, 12, and 24 gN·m-2·a-1 (denoted as CK, C1, C2, and C3, respectively). The results showed that a high-level N (24 gN·m-2·a-1) input could significantly reduce the Chao index and ACE index for the bacterial community and inhibit some dominant microorganisms. The RDA results indicated that TN and NH4+ were the critical factors influencing the soil microbial community under the long-term N input. Moreover, the long-term N input was found to significantly reduce the abundance of Azospirillum and Desulfovibrio, which were typical N-fixing microorganisms. Conversely, the long-term N input was found to significantly increase the abundance of Nitrosospira and Clostridium_sensu_stricto_1, which were typical nitrifying and denitrifying microorganisms. Increased soil N content has been suggested to inhibit the N fixation function of the wetland and exert a positive effect on the processes of nitrification and denitrification in the wetland ecosystem. Our research can be used to improve strategies to protect wetland health.

Effects of sulfadiazine and Cu on soil potential nitrification and ammonia-oxidizing archaea and bacteria communities across different soils

Introduction

Sulfadiazine (SDZ) and copper (Cu) are frequently detected in agricultural soils, but little is known on their single or combined impact on ammonia oxidizing microbial community and function across different soils.

Methods

In this study, a microcosm was conducted to distinguish the microbial ecotoxicity of SDZ and Cu across different soils by analyzing soil potential nitrification rate (PNR) and the amoA gene sequences.

Results

The results showed that the single spiking of SDZ caused a consistent decrease of soil PNR among three tested soils, but no consistent synergistic inhibition of SDZ and Cu was observed across these soils. Moreover, across three tested soils, the distinct responses to the single or joint exposure of SDZ and Cu were found in amoA gene abundance, and diversity as well as the identified genus taxa of ammonia-oxidizing archaea (AOA) and bacteria (AOB). Meanwhile, only the specific genus taxa of AOA or AOB consistently corresponded to the variation of soil PNR across different treated soils. The further principal component analysis (PCA) exhibited that the variable influence of SDZ and Cu on ammonia oxidizing microbial community and function was greatly dependent on soil type.

Discussion

Therefore, in addition to ecological functionality and the specific prokaryotic taxa, soil microbial ecotoxicity of SDZ and Cu also was dependent on edaphic factors derived from soil types. This study proposes an integrative assessment of soil properties and multiple microbial targets to soil contamination management.

The Fashion Industry Needs Microbiology: Opportunities and Challenges

The fashion industry is the second most polluting industry in the world, representing a 2 trillion dollars and growing valuation. Fashion design practices have been perpetuating an industrial-focused approach, which relies mostly in the economic improvement through fast cycles of product development. Additionally, the fashion industry has also been closed to either multidisciplinary or transdisciplinary initiatives outside the scope of the artistic disciplines. Therefore, innovative approaches are needed to solve fashion industrial challenges. One of the most promising fields to tackle current environmental and technological problems in the fashion industry is microbiology. Through the emergent field of synthetic biology, the number of tools and approaches available is increasing and they can already be seen in niche applications. Despite the current advances and urgent need for change, there is still a long way until a more sustainable fashion industry is achieved.

Soil Chemistry and Soil History Significantly Structure Oomycete Communities in Brassicaceae Crop Rotations

Oomycetes are critically important in soil microbial communities, especially for agriculture, where they are responsible for major declines in yields. Unfortunately, oomycetes are vastly understudied compared to bacteria and fungi. As such, our understanding of how oomycete biodiversity and community structure vary through time in the soil remains poor. Soil history established by previous crops is one factor known to structure other soil microbes, but this has not been investigated for its influence on oomycetes. In this study, we established three different soil histories in field trials; the following year, these plots were planted with five different Brassicaceae crops. We hypothesized that the previously established soil histories would structure different oomycete communities, regardless of their current Brassicaceae crop host, in both the roots and rhizosphere. We used a nested internal transcribed spacer amplicon strategy incorporated with MiSeq metabarcoding, where the sequencing data was used to infer amplicon sequence variants of the oomycetes present in each sample. This allowed us to determine the impact of different soil histories on the structure and biodiversity of the oomycete root and rhizosphere communities from the five different Brassicaceae crops. We found that each soil history structured distinct oomycete rhizosphere communities, regardless of different Brassicaceae crop hosts, while soil chemistry structured the oomycete communities more during a dry year. Interestingly, soil history appeared specific to oomycetes but was less influential for bacterial communities previously identified from the same samples. These results advance our understanding of how different agricultural practices and inputs can alter edaphic factors to impact future oomycete communities. Examining how different soil histories endure and impact oomycete biodiversity will help clarify how these important communities may be assembled in agricultural soils. IMPORTANCE Oomycetes cause global plant diseases that result in substantial losses, yet they are highly understudied compared to other microbes, like fungi and bacteria. We wanted to investigate how past soil events, like changing crops in rotation, would impact subsequent oomycete communities. We planted different oilseed crops in three different soil histories and found that each soil history structured a distinct oomycete community regardless of which new oilseed crop was planted, e.g., oomycete communities from last year's lentil plots were still detected the following year regardless of which new oilseed crops we planted. This study demonstrated how different agricultural practices can impact future microbial communities differently. Our results also highlight the need for continued monitoring of oomycete biodiversity and quantification.

The dependent correlation between soil multifunctionality and bacterial community across different farmland soils

Introduction

Microorganisms play a critical role in soil biogeochemical cycles, but it is still debated whether they influence soil biogeochemical processes through community composition and diversity or not. This study aims to investigate variation in bacterial community structure across different soils and its correlation to soil multifunctionality. Soil samples were collected from five typical farmland zones along distinct climatic gradients in China.

Methods

The high-throughput sequencing (Illumina MiSeq) of 16S rRNA genes was employed to analyze bacterial community composition in each soil sample. Multivariate analysis was used to determine the difference in soil properties, microbial community and functioning, and their interactions.

Results

Cluster and discrimination analysis indicated that bacterial community composition was similar in five tested soil samples, but bacterial richness combined with soil enzyme activities and potential nitrification rate (PNR) contributed most to the differentiations of soil samples. Mantel test analysis revealed that bacterial community composition and richness were more significantly shaped by soil nutrient conditions and edaphic variables than bacterial diversity. As for soil multifunctionality, soil microbial community level physiological profiles were little affected by abiotic and biotic factors, while soil enzymes and PNR were also significantly related to bacterial community composition and richness, in addition to soil N and P availability.

Conclusion

Cumulatively, soil enzymes' activities and PNR were greatly dependent on bacterial community composition and richness not diversity, which in turn were greatly modified by soil N and P availability. Therefore, in the future it should be considered for the role of fertilization in the modification of bacterial community and the consequent control of nutrient cycling in soil.

Microbiome-based solutions to address new and existing threats to food security, nutrition, health and agrifood systems' sustainability

In addition to challenges like climate change and biodiversity loss, the sustainability and resilience of agrifood systems worldwide are currently challenged by new threats, such as the COVID-19 pandemic and the Ukraine war. Furthermore, the resilience and sustainability of our agrifood systems need to be enhanced in ways that simultaneously increase agricultural production, decrease post-harvest food losses and food waste, protect the climate, environment and health, and preserve biodiversity. The precarious situation of agrifood systems is also illustrated by the fact that overall, around 3 billion people worldwide still do not have regular access to a healthy diet. This results in various forms of malnutrition, as well as increasing number of people suffering from overweight and obesity, and diet-related, non-communicable diseases (NCDs) around the world. Findings from microbiome research have shown that the human gut microbiome plays a key role in nutrition and diet-related diseases and thus human health. Furthermore, the microbiome of soils, plants, and animals play an equally important role in environmental health and agricultural production. Upcoming, microbiome-based solutions hold great potential for more resilient, sustainable, and productive agrifood systems and open avenues toward preventive health management. Microbiome-based solutions will also be key to make better use of natural resources and increase the resilience of agrifood systems to future emerging and already-known crises. To realize the promises of microbiome science and innovation, there is a need to invest in enhancing the role of microbiomes in agrifood systems in a holistic One Health approach and to accelerate knowledge translation and implementation.

Physiological Responses of a Diazotrophic Cyanobacterium to Acidification of Paddy Floodwater: N2 Fixation, Photosynthesis, and Oxidative-Antioxidative Characteristics

Long-term of excessive fertilization using nitrogen (N) chemical fertilizer caused the acidification of paddy soils. Presently, the impacts of soil acidification on physiological characteristics of diazotrophic cyanobacteria remain unknown. In order to elucidate this issue, the effects of paddy floodwater acidification on activities of respiration, photosynthetic oxygen evolution, and N₂ fixation of a paddy diazotrophic cyanobacterium Aliinostoc sp. YYLX235 were investigated in this study. In addition, the origination and quenching of intracellular reactive oxygen species (ROS) were analyzed. The acidification of paddy floodwater decreased intracellular pH and interfered in energy flux from light-harvesting chlorophyll antenna to the reaction center of photosystem II (PS II). Activities of respiration, photosynthetic oxygen evolution, and N₂ fixation were decreased by the acidification of paddy floodwater. Accompanied with an increase in ROS, the level of antioxidative system increased. Superoxide dismutase (SOD) and catalase (CAT) were the main enzymatic ROS scavengers in the cells of YYLX235; reduced glutathione (GSH) was the main non-enzymatic antioxidant. Antioxidants and oxidants in the cells of YYLX235 lost balance when the pH of paddy floodwater fell to 5.0 and 4.0, and lipid oxidative damage happened. The results presented in this study suggest that the acidification of paddy soil severely interfered in the photosynthesis of diazotrophic cyanobacteria and induced the production of ROS, which in turn resulted in oxidative damage on diazotrophic cyanobacteria and a decrease in cell vitality.

The role of the biogas slurry microbial communities in suppressing fusarium wilt of cucumber

The clarification of the suppressive effect of biogas slurries (BSs) on soil-borne plant pathogens is needed for their large-scale use as a biocontrol tool in potting soil in order to understand the mechanisms of suppression. In this study, pig manure biogas slurry (PS) and vinasse biogas slurry (VS) were used to conduct assays of pathogen mycelial growth suppression and pot experiment to evaluate their effects on the growth of Fusarium. oxysporum f. sp. cucumerinum (FOC) mycelia and cucumber fusarium wilt. The microbial communities of the PS and VS were deeply analyzed to explore the key taxa and potential mechanisms. Results showed that the PS and VS have similar suppression on FOC mycelia and on the control efficiency, while they were significantly weakened when the PS and VS were used after sterilization. The microbial parameters of the two BSs were obviously different, and functional microbial taxa for disease resistance were observed in the two BSs. Spearman correlation showed that genera of the Pseudomonas, Ochrobactrum, Papiliotrema, etc., were the suppression-related taxa in the PS, while Leucobacter, unclassified_Microbacteriaceae, etc. in the VS. Overall, various key taxa in the PS and VS produced similar suppression on cucumber fusarium wilt.

Effect of the combination of biological, chemical control and agronomic technique in integrated management pea root rot and its productivity

Root rot of pea caused by Fusarium spp. is one of the important diseases of pea (Pisum sativum L.). The causal fungus of the disease isolated from naturally infected pea plants was identified as Fusarium solani f. sp. pisi (Jones). Evaluation of four bio agents and nine fungicides was done in vitro against Fusarium solani. Trichoderma harzianum was the most effective bio agent in inhibiting the mycelial growth of F. solani by (82.62%). Carbendazim 50 WP was the most effective fungicide in inhibiting the mycelial growth of F. solani by (91.06%). Carbendazim at the rate of 0.1% and T. harzianum at concentration of 109 cfu when used as seed treatment under field conditions were evaluated along with three planting techniques v.i.z, raised beds, ridges and flat beds. It was found that Carbendazim at the rate of 0.1% when given as seed treatment in raised beds exhibited the lowest disease incidence (10.97%), intensity (2.89%) and the maximum pod yield (89.63 q ha-1) as compared to control.

Brassicaceae host plants mask the feedback from the previous year's soil history on bacterial communities, except when they experience drought

Soil history operates through time to influence the structure and biodiversity of soil bacterial communities. Examining how different soil histories endure will help clarify the rules of bacterial community assembly. In this study, we established three different soil histories in field trials; the following year these plots were planted with five different Brassicaceae species. We hypothesized that the previously established soil histories would continue to structure the subsequent Brassicaceae bacterial root and rhizosphere communities. We used a MiSeq 16S rRNA metabarcoding strategy to determine the impact of different soil histories on the structure and biodiversity of the bacterial root and rhizosphere communities from the five different Brassicaceae host plants. We found that the Brassicaceae hosts were consistently significant factors in structuring the bacterial communities. Four host plants (Sinapis alba, Brassica napus, B. juncea, B. carinata) formed similar bacterial communities, regardless of different soil histories. Camelina sativa host plants structured phylogenetically distinct bacterial communities compared to the other hosts, particularly in their roots. Soil history established the previous year was only a significant factor for bacterial community structure when the feedback of the Brassicaceae host plants was weakened, potentially due to limited soil moisture during a dry year. Understanding how soil history is involved in the structure and biodiversity of bacterial communities through time is a limitation in microbial ecology and is required for employing microbiome technologies in improving agricultural systems. This article is protected by copyright. All rights reserved.

The Soil Microbiota Recovery in the Agroecosystem: Minimal Information and a New Framework for Sustainable Agriculture

The efficient management of soil represents a mission of vital importance for meeting the continuously increasing agricultural demand in a sustainable way. Decades of research identified in the biotechnological potential of soil microorganisms an always more practicable channel for achieving these goals. Due to the complexity of soil microbial communities and their tight connection to soil characteristics, it is still difficult to define universal strategies for an efficient and sustainable agroecosystem management. We here propose a new framework for the assessment of the impact of agricultural practices in the agroecosystem that revolves around the concept of microbial community recovery. This assessment is based on the selection of (i) a representative temporal interval, (ii) a representative agricultural system and (iii) monitoring tools able to assess the expression levels of microbial functionality in soil. This approach can be especially valuable for evaluating the effects of agrochemicals and other agronomical amendments (of different nature: biological, physical, chemical) on the soil microbiota. In the same way precision-medicine tries to tailor drugs on an always smaller subset of patients' characteristics, a new generation of agrochemicals can be developed and tested considering soil characteristics in order to minimize their off-target effects. What remains central in this paradigm is the promotion of Soil Health maintenance practices. As for healthy humans, a healthy soil is more resilient and tolerates treatments and stresses better while recovering more quickly.

Fungal Inhibition of Agricultural Soil Pathogen Stimulated by Nitrogen-Reducing Fertilization

Plant health is the fundamental of agricultural production, which is threatened by plant pathogens severely. The previous studies exhibited the effects of different pathogen control strategies (physical, chemical, and microbial methods), which resulted from bringing in exogenous additives, on microbial community structures and functions. Nevertheless, few studies focused on the potential inhibitory abilities of native microbial community in the soil, which could be activated or enhanced by different fertilization strategies. In this study, three plant diseases (TMV, TBS, and TBW) of tobacco, fungal community of tobacco rhizosphere soil, and the correlation between them were researched. The results showed that nitrogen-reducing fertilization strategies could significantly decrease the occurrence rate and the disease index of three tobacco diseases. The results of bioinformatics analyses revealed that the fungal communities of different treatments could differentiate the nitrogen-reducing fertilization group and the control group (CK). Furthermore, key genera which were responsible for the variation of fungal community were explored by LEfSe analysis. For instance, Tausonia and Trichocladium increased, while Naganishia and Fusicolla decreased under nitrogen-reducing fertilization conditions. Additionally, the correlation between tobacco diseases and key genera was verified using the Mantel test. Moreover, the causal relationship between key genera and tobacco diseases was deeply explored by PLS–PM analysis. These findings provide a theoretical basis for a nitrogen-reducing fertilization strategy against tobacco diseases without exogenous additives and make contributions to revealing the microbial mechanism of native-valued fungal key taxa against tobacco diseases, which could be stimulated by agricultural fertilization management.

Effects of Soil Quality on the Microbial Community Structure of Poorly Evolved Mediterranean Soils

Physical and chemical alterations may affect the microbiota of soils as much as the specific presence of toxic pollutants. The relationship between the microbial diversity patterns and the soil quality in a Mediterranean context is studied here to test the hypothesis that soil microbiota is strongly affected by the level of anthropogenic soil alteration. Our aim has been to determine the potential effect of organic matter loss and associated changes in soil microbiota of poorly evolved Mediterranean soils (Leptosols and Regosols) suffering anthropogenic stress (i.e., cropping and deforestation). The studied soils correspond to nine different sites which differed in some features, such as the parent material, vegetation cover, or soil use and types. A methodological approach has been used that combines the classical physical and chemical study of soils with molecular characterization of the microbial assemblages using specific primers for Bacteria, Archaea and ectomycorrhizal Fungi. In agreement with previous studies within the region, physical, chemical and biological characteristics of soils varied notably depending on these factors. Microbial biomass, soil organic matter, and moisture, decreased in soils as deforestation increased, even in those partially degraded to substitution shrubland. Major differences were observed in the microbial community structure between the mollic and rendzic Leptosols found in forest soils, and the skeletic and dolomitic Leptosols in substitute shrublands, as well as with the skeletic and dolomitic Leptosols and calcaric Regosols in dry croplands. Forest soils displayed a higher microbial richness (OTU’s number) and biomass, as well as more stable and connected ecological networks. Here, we point out how human activities such as agriculture and other effects of deforestation led to changes in soil properties, thus affecting its quality driving changes in their microbial diversity and biomass patterns. Our findings demonstrate the potential risk that the replacement of forest areas may have in the conservation of the soil’s microbiota pool, both active and passive, which are basic for the maintenance of biogeochemical processes.

Effects of Abiotic Stress on Soil Microbiome

Rhizospheric organisms have a unique manner of existence since many factors can influence the shape of the microbiome. As we all know, harnessing the interaction between soil microbes and plants is critical for sustainable agriculture and ecosystems. We can achieve sustainable agricultural practice by incorporating plant-microbiome interaction as a positive technology. The contribution of this interaction has piqued the interest of experts, who plan to do more research using beneficial microorganism in order to accomplish this vision. Plants engage in a wide range of interrelationship with soil microorganism, spanning the entire spectrum of ecological potential which can be mutualistic, commensal, neutral, exploitative, or competitive. Mutualistic microorganism found in plant-associated microbial communities assist their host in a number of ways. Many studies have demonstrated that the soil microbiome may provide significant advantages to the host plant. However, various soil conditions (pH, temperature, oxygen, physics-chemistry and moisture), soil environments (drought, submergence, metal toxicity and salinity), plant types/genotype, and agricultural practices may result in distinct microbial composition and characteristics, as well as its mechanism to promote plant development and defence against all these stressors. In this paper, we provide an in-depth overview of how the above factors are able to affect the soil microbial structure and communities and change above and below ground interactions. Future prospects will also be discussed.