Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators

Forest-to-Cropland Conversion Reshapes Microbial Hierarchical Interactions and Degrades Ecosystem Multifunctionality at a National Scale

Conversion from natural lands to cropland, primarily driven by agricultural expansion, could significantly alter soil microbiome worldwide; however, influences of forest-to-cropland conversion on microbial hierarchical interactions and ecosystem multifunctionality have not been fully understood. Here, we examined the effects of forest-to-cropland conversion on intratrophic and cross-trophic microbial interactions and soil ecosystem multifunctionality and further disclosed their underlying drivers at a national scale, using Illumina sequencing combined with high-throughput quantitative PCR techniques. The forest-to-cropland conversion significantly changed the structure of soil microbiome (including prokaryotic, fungal, and protistan communities) while it did not affect its alpha diversity. Both intrakingdom and interkingdom microbial networks revealed that the intratrophic and cross-trophic microbial interaction patterns generally tended to be more modular to resist environmental disturbance introduced from forest-to-cropland conversion, but this was insufficient for the cross-trophic interactions to maintain stability; hence, the protistan predation behaviors were still disturbed under such conversion. Moreover, key soil microbial clusters were declined during the forest-to-cropland conversion mainly because of the increased soil total phosphorus level, and this drove a great degradation of the ecosystem multifunctionality (by 207%) in cropland soils. Overall, these findings comprehensively implied the negative effects of forest-to-cropland conversion on the agroecosystem, from microbial hierarchical interactions to ecosystem multifunctionality.

Decomposing benefits: Examining the impact of beech deadwood on soil properties and microbial diversity

Deadwood is an important element of forest ecosystems that affects many of its components, including the soil environment. Our research is an attempt to determine the role of decaying wood in shaping the properties of forest soils in mountain ecosystems. The aim of our research was to present the influence of beech deadwood on physicochemical properties and microbiological diversity of soils. The research was carried out in the Baba Góra Massif at its northern exposure. The research plots were established in the altitude gradient at 600, 800 and 1000 m above sea level. On each plot, samples were taken from decaying wood, from the soil directly under the decaying log, and a soil sample 1 m from the log as a control. We determined the basic properties of the samples, that is pH, C and N concentration and lignin content. The enzymatic activity and additionally, the taxonomic composition of soil bacterial and fungal communities was determined in the collected samples. Our research indicates the important role of decaying beech wood in shaping the properties of forest soils. We noted a positive effect of decaying wood on the properties of the tested soils. Soils affected by deadwood were characterized by significantly higher pH, C and N concentrations compared to control soils, regardless of their location in the altitude gradient. Additionally, we found that soils affected by decaying wood are characterized by a different composition of microorganisms regardless of their location in the altitude gradient. In control soil the fungal and bacterial alpha diversity were lowest compared with the deadwood and soil under the influence of deadwood. Our results may have practical applications in the management of forest ecosystems. The presented results indicate the possibility of leaving deadwood in order to improve its basic physicochemical properties and increase microbial diversity.

Biochemical and nanotechnological approaches to combat phytoparasitic nematodes

The foundation of most food production systems underpinning global food security is the careful management of soil resources. Embedded in the concept of soil health is the impact of diverse soil-borne pests and pathogens, and phytoparasitic nematodes represent a particular challenge. Root-knot nematodes and cyst nematodes are severe threats to agriculture, accounting for annual yield losses of US$157 billion. The control of soil-borne phytoparasitic nematodes conventionally relies on the use of chemical nematicides, which can have adverse effects on the environment and human health due to their persistence in soil, plants, and water. Nematode-resistant plants offer a promising alternative, but genetic resistance is species-dependent, limited to a few crops, and breeding and deploying resistant cultivars often takes years. Novel approaches for the control of phytoparasitic nematodes are therefore required, those that specifically target these parasites in the ground whilst minimizing the impact on the environment, agricultural ecosystems, and human health. In addition to the development of next-generation, environmentally safer nematicides, promising biochemical strategies include the combination of RNA interference (RNAi) with nanomaterials that ensure the targeted delivery and controlled release of double-stranded RNA. Genome sequencing has identified more than 75 genes in root knot and cyst nematodes that have been targeted with RNAi so far. But despite encouraging results, the delivery of dsRNA to nematodes in the soil remains inefficient. In this review article, we describe the state-of-the-art RNAi approaches targeting phytoparasitic nematodes and consider the potential benefits of nanotechnology to improve dsRNA delivery.

Tea and Pleurotus ostreatus intercropping modulates structure of soil and root microbial communities

Intercropping with Pleurotus ostreatus has been demonstrated to increase the tea yield and alleviate soil acidification in tea gardens. However, the underlying mechanisms remain elusive. Here, high-throughput sequencing and Biolog Eco analysis were performed to identify changes in the community structure and abundance of soil microorganisms in the P. ostreatus intercropped tea garden at different seasons (April and September). The results showed that the soil microbial diversity of rhizosphere decreased in April, while rhizosphere and non-rhizosphere soil microbial diversity increased in September in the P. ostreatus intercropped tea garden. The diversity of tea tree root microorganisms increased in both periods. In addition, the number of fungi associated with organic matter decomposition and nutrient cycling, such as Penicillium, Trichoderma, and Trechispora, was significantly higher in the intercropped group than in the control group. Intercropping with P. ostreatus increased the levels of total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) in the soil. It also improved the content of secondary metabolites, such as tea catechins, and polysaccharides in tea buds. Microbial network analysis showed that Unclassified_o__Helotiales, and Devosia were positively correlated with soil TN and pH, while Lactobacillus, Acidothermus, and Monascus were positively correlated with flavone, AE, and catechins in tea trees. In conclusion, intercropping with P. ostreatus can improve the physical and chemical properties of soil and the composition and structure of microbial communities in tea gardens, which has significant potential for application in monoculture tea gardens with acidic soils.

Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence

BACKGROUND

Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing.

RESULTS

Fungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion.

CONCLUSIONS

Microbial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.

Bacterial diversity in agricultural drainage ditches shifts with increasing urea-N concentrations

Urea-based fertilizers applied to crop fields can enter the surface waters of adjacent agricultural drainage ditches and contribute to the nitrogen (N) loading in nearby watersheds. Management practices applied in drainage ditches promote N removal by the bacterial communities, but little is known about the impacts of excess urea fertilizer from crop fields on the bacterial diversity in these ditches. In 2017, sediments from drainage ditches next to corn and soybean fields were sampled to determine if fertilizer application and high urea-N concentrations alters bacterial diversity and urease gene abundances. A mesocosm experiment was paired with a field study to determine which bacterial groups respond to high urea-N concentrations. The bacterial diversity in the ditch next to corn fields was significantly different from the other site. The bacterial orders of Rhizobiales, Bacteroidales, Acidobacteriales, Burkholderiales, and Anaerolineales were most abundant in the ditch next to corn and increased after the addition of urea-N (0.5 mg N L-1) during the mesocosm experiment. The results of our study suggests that urea-N concentrations >0.07 mg N L-1, which are higher than concentrations associated with downstream harmful algal blooms, can lead to shifts in the bacterial communities of agricultural drainage ditches.

Deforestation impacts soil biodiversity and ecosystem services worldwide

Deforestation poses a global threat to biodiversity and its capacity to deliver ecosystem services. Yet, the impacts of deforestation on soil biodiversity and its associated ecosystem services remain virtually unknown. We generated a global dataset including 696 paired-site observations to investigate how native forest conversion to other land uses affects soil properties, biodiversity, and functions associated with the delivery of multiple ecosystem services. The conversion of native forests to plantations, grasslands, and croplands resulted in higher bacterial diversity and more homogeneous fungal communities dominated by pathogens and with a lower abundance of symbionts. Such conversions also resulted in significant reductions in carbon storage, nutrient cycling, and soil functional rates related to organic matter decomposition. Responses of the microbial community to deforestation, including bacterial and fungal diversity and fungal guilds, were predominantly regulated by changes in soil pH and total phosphorus. Moreover, we found that soil fungal diversity and functioning in warmer and wetter native forests is especially vulnerable to deforestation. Our work highlights that the loss of native forests to managed ecosystems poses a major global threat to the biodiversity and functioning of soils and their capacity to deliver ecosystem services.

Neutral diversity in experimental metapopulations

New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial populations are grown in parallel serial transfers, in some cases with population-wide extinction and splitting events. We model bacterial growth by a birth-death process and use the theory of coalescent point processes. We show that there is a dilution factor that optimises the expected amount of neutral diversity for a given number of cycles, and study the power law behaviour of the mutation frequency spectrum for different experimental regimes. We also explore how neutral variation diverges between two recently split populations by establishing a new formula for the expected number of shared and private mutations. Finally, we show the interest of such a setup to select a phenotype of interest that requires multiple mutations.

Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales

The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.

Chemical composition of soil carbon is governed by microbial diversity during understory fern removal in subtropical pine forests

Understory vegetation has an important impact on soil organic carbon (SOC) accumulation. However, little is known about how understory vegetation alters soil microbial community composition and how microbial diversity contributes to SOC chemical composition and persistence during subtropical forest restoration. In this study, removal treatments of an understory fern (Dicranopteris dichotoma) were carried out within pine (Pinus massoniana) plantations restored in different years in subtropical China. Soil microbial community composition and microbial diversity were measured using phospholipid fatty acids (PLFAs) biomarkers and high-throughput sequencing, respectively. The chemical composition of SOC was also measured via solid-state 13C nuclear magnetic resonance (13C NMR). Our results showed that fern removal decreased alkyl C by 4.2 % but increased O-alkyl C by 15.6 % on average, leading to a decline of alkyl C/O-alkyl C ratio, suggesting altered chemical composition of SOC and lowered SOC recalcitrance without fern. Fern removal significantly lowered the fungi-to-bacteria ratio, and it also reduced fungal and bacterial diversity. Partial correlation analysis revealed that soil nitrogen availability was a key factor influencing microbial diversity. Bacterial diversity showed a close relationship with the Alkyl C/O-alkyl C ratio following fern removal. Furthermore, the microbial community structure and bacterial diversity were responsible for 18 % and 55 % of the explained variance in the chemical composition of SOC, respectively. Taken together, these analyses jointly suggest that bacterial diversity exerts a greater role than microbial community structure in supporting SOC persistence during understory fern removal. Our study emphasizes the significance of understory ferns in supporting microbial abundance and diversity as a means of altering SOC persistence during subtropical forest restoration.

Microorganism community structure: A characterisation of agrosystems from Madeira Archipelago

Microbial diversity profoundly influences soil ecosystem functions, making it vital to monitor community dynamics to comprehend its structure. Our study focused on six agrosystems in Madeira Archipelago, analysing bacteria, archaea, fungi and AMF through classical microbiology and molecular techniques. Despite distinct edaphoclimatic conditions and management practices, bacterial structures exhibited similarities, with Alphaproteobacteria at 18%-20%, Bacilli at 11%-18% and Clostridia at 9%-14%. The predominance of copiothrophic groups suggested that soil nutrient content was the driver of these communities. Regarding archaea, the communities changed among sites, and it was evident that agrosystems provided niches for methanogens. The Crenarchaeota varied between 15% and 29%, followed by two classes of Euryarchaeota, Methanomicrobia (17%-25%) and Methanococci (4%-32%). Fungal communities showed consistent composition at the class level but had differing diversity indices due to management practices and soil texture. Sordaryomycetes (21%-28%) and Agaricomycetes (15%-23%) were predominant. Conversely, AMF communities appeared to be also influenced by the agrosystem, with Glomus representing over 50% of the community in all agrosystems. These insights into microbial groups' susceptibilities to environmental conditions are crucial for maintaining healthy soil and predicting climate change effects on agrosystems' productivity, resilience and sustainability. Additionally, our findings enable the development of more robust prediction models for agricultural practices.

Effects of in situ Fe oxide precipitation on As stabilization and soil ecological resilience under salt stress

Iron (Fe) oxide precipitation is a promising method for stabilizing arsenic (As) in contaminated soils; however, the addition of salts during the process can negatively affect soil functions. This study investigated the effects of in situ Fe oxide precipitation on As stabilization and the impact of salt stress on soil functions and microbial communities. Fe oxide precipitation reduced the concentration of bioaccessible As by 84% in the stabilized soil, resulting in the formation of ferrihydrite and lepidocrocite, as confirmed by XANES. Nevertheless, an increase in salt stress reduced barley development, microbial enzyme activities, and microbial diversity compared to those in the original soil. Despite this, the stabilized soil exhibited natural resilience and potential for enhanced microbial adaptations, with increased retention of salt-tolerant bacteria. Washing the stabilized soil with water restored EC1:5 to the level of the original soil, resulting in increased barley growth rates and enzyme activities after 5-d and 20-week incubation periods, suggesting soil function recovery. 16 S rRNA sequencing revealed the retention of salt-tolerant bacteria in the stabilized soil, while salt-removed soil exhibited an increase in Proteobacteria, which could facilitate ecological functions. Overall, Fe oxide precipitation effectively stabilized soil As and exhibited potential for restoring the natural resilience and ecological functions of soils through microbial adaptations and salt removal.

Microbial transformation of soil organic matter under varying agricultural management systems in Ukraine

Introduction

This paper presents comparative studies on the content and structure of organic matter (OM) and the activity of microbiological cellulose destruction in three types of Ukrainian soils intensively used in agricultural production.

Methods

The highest content of humus in the arable layer (4.9%), OM (410 t ha-1), and total carbon (30.9 mg C g-1 soil) was determined in chernic phaeozems, which is 2.2-2.5 times higher than in albic retisols. The soil of natural ecosystems is characterised by a high content of microbial carbon (Cmic) in the carbon fraction of organic soil compounds.

Results and discussion

In arable soils, the content and reserves of humus and soil organic matter (SOM) have decreased by an average of 1.5-2 times. The most considerable loss of humus reserves in the soil profile was identified in albic retisols (1.96-1.44 times) and the smallest in chernic phaeozems (1.27-1.81 times). During the long-term systematic application of mineral fertilisers, the Corg content decreased by 8-21% in chernic phaeozems, 12-33% in greyzemic phaeozems, and 6-38% in albic retisols. A significant difference of 2.1-8.0 times was determined regarding the number of aerobic cellulolytic microorganisms and 1.3-3.3 times in the potential cellulolytic activity of the studied soils. The high number of cellulose-destroying microorganisms is characteristic of chernic phaeozems with a high content of OM in the soil; the advantage over other types of studied soils was 1.4 times and 7.8 times for greyzemic phaeozems and albic retisols, respectively. Among the studied soil types, high values of CO2 emissions were identified in chernic phaeozems. Intensive agricultural practices in Ukrainian soils have significantly altered the content and composition of organic matter, leading to reduced humus and soil organic matter reserves. The study also underscores the importance of considering the abundance of cellulose-destroying microorganisms and their potential activity in assessing soil health and sustainability.

Soil bacterial community composition in rice-turtle coculture systems with different planting years

The rice-turtle coculture system is the most special rice-fish integrated farming system. In this study, we selected four paddy fields, including a rice monoculture paddy and three rice-turtle paddies with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the contents of soil available nitrogen (AN), soil available phosphorus (AP) and soil organic matter (OM) in 9th year of rice-turtle paddy (RT9) were increased by 5.40%, 51.11% and 23.33% compared with rice monoculture paddy (CK), respectively. Significant differences of Acidobacteria, Desulfobacteria, Crenarchaeota were observed among the different rice farming systems. The relative abundance of Methylomonadaceae, Methylococcaceae and Methylophilaceae in RT9 was significantly higher than that in other treatments. RT9 had significantly lower relative abundance of Acidobacteria, but significantly higher relative abundance of Proteobacteria than other treatments. Redundancy analysis showed that soil AN and AP contents were the major factors influencing the abundance of the dominant microbes, wherein Methylomonadaceae, Methylococcaceae and Methylophilaceae were positively correlated with OM. The findings revealed the rice-turtle coculture system in the 9th year had higher soil nutrients and soil bacterial diversity, but there was also a risk of increasing methane emissions.

Land use conversion increases network complexity and stability of soil microbial communities in a temperate grassland

Soils harbor highly diverse microbial communities that are critical to soil health, but agriculture has caused extensive land use conversion resulting in negative effects on critical ecosystem processes. However, the responses and adaptations of microbial communities to land use conversion have not yet been understood. Here, we examined the effects of land conversion for long-term crop use on the network complexity and stability of soil microbial communities over 19 months. Despite reduced microbial biodiversity in comparison with native tallgrass prairie, conventionally tilled (CT) cropland significantly increased network complexity such as connectivity, connectance, average clustering coefficient, relative modularity, and the number of species acting at network hubs and connectors as well as resulted in greater temporal variation of complexity indices. Molecular ecological networks under CT cropland became significantly more robust and less vulnerable, overall increasing network stability. The relationship between network complexity and stability was also substantially strengthened due to land use conversion. Lastly, CT cropland decreased the number of relationships between network structure and environmental properties instead being strongly correlated to management disturbances. These results indicate that agricultural disturbance generally increases the complexity and stability of species "interactions", possibly as a trade-off for biodiversity loss to support ecosystem function when faced with frequent agricultural disturbance.

Assembly and co-occurrence patterns of rhizosphere bacterial communities are closely linked to soil fertility during continuous cropping of cut chrysanthemum (Chrysanthemum morifolium Ramat)

AIMS

Continuous cropping is known to have profound effects on the soil microbial community in different planting systems. However, we lack an understanding of how different years of continuous cropping affects rhizosphere soil bacterial community co-occurrence pattern and assembly processes in the cut chrysanthemum (Chrysanthemum morifolium Ramat.) field.

METHODS AND RESULTS

We collected the soils from cut chrysanthemum rhizospheres with planting for 1 year (PY1) and continuous cropping for 6 years (CY6) and 12 years (CY12). Real-time quantitative PCR and flow cytometry (FCM) techniques were used to test the 16S rRNA gene copy number and bacterial cell count, respectively. The bacterial community structure was analysed by using high-throughput sequencing technology. The CY12 had a significantly decreased soil fertility index and rhizosphere bacterial living cell counts and gene copy numbers compared to CY6 and PY1 (P < 0.05). The rhizosphere bacterial community dissimilarity increased as the continuous cropping years increased. Three main ecological clusters (modules #1, #2, and #3) were observed in the bacterial co-occurrence network across all samples, and only the relative abundance of module #1 (enriched in the CY12) was significantly correlated with soil fertility (P < 0.05). Moreover, the rhizosphere bacterial community assembly was primarily governed by the deterministic process under 12 years of continuous cropping.

CONCLUSIONS

Soil fertility decline correlates with ecological network modularization and the deterministic assembly process of the rhizosphere bacterial community of cut chrysanthemum during continuous cropping.

Thriving beneath olive trees: The influence of organic farming on microbial communities

Soil health and root-associated microbiome are interconnected factors involved in plant health. The use of manure amendment on agricultural fields exerts a direct benefit on soil nutrient content and water retention, among others. However, little is known about the impact of manure amendment on the root-associated microbiome, particularly in woody species. In this study, we aimed to evaluate the effects of ovine manure on the microbial communities of the olive rhizosphere and root endosphere. Two adjacent orchards subjected to conventional (CM) and organic (OM) management were selected. We used metabarcoding sequencing to assess the bacterial and fungal communities. Our results point out a clear effect of manure amendment on the microbial community. Fungal richness and diversity were increased in the rhizosphere. The fungal biomass in the rhizosphere was more than doubled, ranging from 1.72 × 10⁶ ± 1.62 × 10⁵ (CM) to 4.54 × 10⁶ ± 8.07 × 10⁵ (OM) copies of the 18 S rRNA gene g^-1 soil. Soil nutrient content was also enhanced in the OM orchard. Specifically, oxidable organic matter, total nitrogen, nitrate, phosphorous, potassium and sulfate concentrations were significantly increased in the OM orchard. Moreover, we predicted a higher abundance of bacteria in OM with metabolic functions involved in pollutant degradation and defence against pathogens. Lastly, microbial co-occurrence network showed more positive interactions, complexity and shorter geodesic distance in the OM orchard. According to our results, manure amendment on olive orchards represents a promising tool for positively modulating the microbial community in direct contact with the plant.

Metagenomic analysis of antimicrobial resistance in ducks, workers, and the environment in duck farms, southern China

Duck farms are one of the important reservoirs of antimicrobial resistance genes (ARGs) that spread to humans and the environment. However, few studies have focused on the characteristics of antimicrobial profiles in duck farms. Here we explored the distribution characteristics and potential transmission mechanisms of ARGs in ducks, farm workers, and the environment in duck farms by a metagenomic approach. The results showed that the highest abundance and diversity of ARGs were found in duck manure. The abundance and diversity of ARGs in workers and environmental samples were higher than those in the control group. tet(X) and its variants were prevalent in duck farms, with tet(X10) being the most abundant. The genetic structure "tet(X)-like + α/β hydrolase" was found in ducks, workers, and the environment, implying that tet(X) and its variants have been widely spread in duck farms. Network analysis indicated that ISVsa3 and IS5075 might play an important role in the coexistence of ARGs and metal resistance genes (MRGs). The Mantel tests showed that mobile genetic elements (MGEs) were significantly correlated with ARG profiles. The results suggest that duck manure may be a potential hotspot source of ARGs, including tet(X) variants that spread to the surrounding environment and workers via MGEs. These results help us optimize the antimicrobials strategy and deepen our understanding of ARG spread in duck farms.

Insights into the driving factors of vertical distribution of antibiotic resistance genes in long-term fertilized soils

The prevalence of antibiotic resistance genes (ARGs) in soils has aroused wide attention. However, the influence of long-term fertilization on the distribution of ARGs in different soil layers and its dominant drivers remain largely unknown. In this study, a total of 203 ARGs were analyzed in greenhouse vegetable soils (0-100 cm from a 13-year field experiment applied with different fertilizers (control, chemical fertilizer, organic manure, and mixed fertilizer). Compared with unfertilized and chemically fertilized soils, manure application significantly increased the abundance and alpha diversity of soil ARGs, where the assembly of ARG communities was strongly driven by stochastic processes. The distribution of ARGs was significantly driven by manure application within 60 cm, while it was insignificantly changed in soil below 60 cm under different fertilization regimes. The inter-correlations of ARGs with mobile genetic elements (MGEs) and microbiota were strengthened in manured soil, indicating manure application posed a higher risk for ARGs diffusion in subsurface soil. Bacteria abundance and MGEs directly influenced ARG abundance and composition, whereas soil depth and manure application indirectly influenced ARG abundance and composition by affecting antibiotics. These results strengthen our understanding of the long-term anthropogenic influence on the vertical distribution of soil ARGs and highlight the ecological risk of ARGs in subsurface soil induced by long-term manure application.

Soil Bacterial Assemblage Across a Production Landscape: Agriculture Increases Diversity While Revegetation Recovers Community Composition

Aboveground ecological impacts associated with agricultural land use change are evident as natural plant communities are replaced with managed production systems. These impacts have been extensively studied, unlike those belowground, which remain poorly understood. Soil bacteria are good candidates to monitor belowground ecological dynamics due to their prevalence within the soil system and ability to survive under harsh and changing conditions. Here, we use soil physicochemical assessment and 16S rRNA gene sequencing to investigate the soil physical and bacterial assemblage changes across a mixed-use agricultural landscape. We assess soil from remnant vegetation (Eucalyptus mallee), new and old vineyards, old pasture, and recently revegetated areas. Elevated concentrations of nitrogen (NO₃^-) and plant-available (Colwell) phosphorus were identified in the managed vineyard systems, highlighting the impact of agricultural inputs on soil nutrition. Alpha diversity comparison revealed a significant difference between the remnant mallee vegetation and the vineyard systems, with vineyards supporting highest bacterial diversity. Bacterial community composition of recently revegetated areas was similar to remnant vegetation systems, suggesting that bacterial communities can respond quickly to aboveground changes, and that actions taken to restore native plant communities may also act to recover natural microbial communities, with implications for soil and plant health. Findings here suggest that agriculture may disrupt the correlation between above- and belowground diversities by altering the natural processes that otherwise govern this relationship (e.g. disturbance, plant production, diversity of inputs), leading to the promotion of belowground microbial diversity in agricultural systems.

Microalgae as next generation plant growth additives: Functions, applications, challenges and circular bioeconomy based solutions

Sustainable agriculture practices involve the application of environment-friendly plant growth promoters and additives that do not negatively impact the health of the ecosystem. Stringent regulatory frameworks restricting the use of synthetic agrochemicals and the increase in demand for organically grown crops have paved the way for the development of novel bio-based plant growth promoters. In this context, microalgae biomass and derived agrochemicals offer novel sources of plant growth promotors that enhance crop productivity and impart disease resistance. These beneficial effects could be attributed to the presence of wide range of biomolecules such as soluble amino acid (AA), micronutrients, polysaccharides, phytohormones and other signaling molecules in microalgae biomass. In addition, their phototrophic nature, high photosynthetic efficiency, and wide environmental adaptability make them an attractive source of biostimulants, biofertilizers and biopesticides. The present review aims to describe the various plant growth promoting metabolites produced by microalgae and their effects on plant growth and productivity. Further, the effects elicited by microalgae biostimulants with respect to different modes of applications such as seed treatments, foliar spray and soil/root drenching is reviewed in detail. In addition, the ability of microalgae metabolites to impart tolerance against various abiotic and biotic stressors along with the mechanism of action is discussed in this paper. Although the use of microalgae based biofertilizers and biostimulants is gaining popularity, the high nutrient and water requirements and energy intensive downstream processes makes microalgae based technology commercially unsustainable. Addressing this challenge, we propose a circular economy model of microalgae mediated bioremediation coupled with biorefinery approaches of generating high value metabolites along with biofertilizer applications. We discuss and review new trends in enhancing the sustainability of microalgae biomass production by co-cultivation of algae with hydroponics and utilization of agriculture effluents.

Comparative study of bacterial community dynamics in different soils following application of the herbicide atrazine

Microbial communities in cultivated soils control the fate of pollutants associated with agricultural practice. The present study was designed to explore the response of bacterial communities to the application of the widely-used herbicide atrazine in three different crop fields that differ significantly in their physicochemical structure and nutritional content: the nutrient-rich (with relatively high carbon and nitrogen content) Newe Yaar (NY) and Ha-Ogen (HO) soils and the nutrient-poor, sandy Sde-Eliyahu (SE) soil. The 16 S rRNA gene amplicon sequencing revealed the nutrient poor HO soil differs in its response to atrazine in comparison to the two nutrient-rich soils both in the shortest persistence of atrazine and its effect on community structure and composition. Potential reported bacterial degraders of atrazine such as Pseudomonas, Clostridium and Bacillus were more abundant in contaminated sandy/poor soils (HO) whereas bacteria known for nitrogen cycling such as Azospirillum, Sinorhizobium, Nitrospira and Azohydromonas were significantly more abundant in the nutrient rich contaminated SE soils. No significant increase of potential indigenous degrader Arthrobacter was detected in SE and NY soils whereas a significant increase was recorded with HO soils. An overall shift in bacterial community composition following atrazine application was observed only in the nutrient poor soil. Understanding atrazine persistence and microbiome response to its application of in dependence with soil types serve the design of precision application strategies.

Reducing plant pathogens could increase crop yields after plastic film mulching

Soil fungi are closely associated with crop growth in agricultural ecosystems through processes such as nutrient uptake and pathogenesis. Plastic film mulching (PM) plays a dominant role in increasing crop yields in dryland agriculture worldwide. The functional guilds of soil fungi under PM and their effects on crops remain unclear. In this study, we explored the absolute abundance, diversity, community composition, and functional guilds of soil fungi after short-term (2 years) and long-term (10 years) mulching experiments. Short-term mulching caused a 37 %-51 % decrease in absolute fungal abundance owing to abrupt changes in the microenvironment. The response of the fungal community to PM varied with sites, with the effect being more pronounced under poor hydrothermal conditions (314 mm). The abundance of potential fungal pathogens decreased under PM; for example, Gibberella (maize ear rot) abundance was 45 % and 72 % lower under short- and long-term mulching, respectively, when compared with that in control. In contrast, the abundance of plant biocontrol fungi increased under PM; for instance, Glomeromycota abundance increased twofold under long-term mulching. Although PM did not alter the complexity and stability of fungal co-occurrence network, competition among fungi increased in the absence of sufficient carbon (C) sources. Long-term mulching reduced phytopathogen guilds by 12 %-77 % and increased arbuscular mycorrhizal fungi (AMF) guilds by 89 %-94 %. Structural equation modeling suggested that PM altered fungal functional guilds mainly by shaping the structure of the fungal community, and fungal pathogens decreased with increased AMF functional guilds, inducing higher maize yields. These results showed for the first time, from a microbial perspective, that pathogens reduction owing to PM could explain 4.4 % of maize yield variation, providing theoretical guidance to accomplish sustainability of continuous maize mulching.

Adaptation of Rhizosphere Microbial Communities to Continuous Exposure to Multiple Residual Antibiotics in Vegetable Farms

The constant application of manure-based fertilizers in vegetable farms leads to antibiotic residue accumulation in soils, which has become a major stressor affecting agroecosystem stability. The present study investigated the adaptation profiles of rhizosphere microbial communities in different vegetable farms to multiple residual antibiotics. Multiple antibiotics, including trimethoprim, sulfonamides, quinolones, tetracyclines, macrolides, lincomycins, and chloramphenicols, were detected in the vegetable farms; the dominant antibiotic (trimethoprim) had a maximum concentration of 36.7 ng/g. Quinolones and tetracyclines were the most prevalent antibiotics in the vegetable farms. The five most abundant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Firmicutes, while the five most abundant phyla in root samples were Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Myxococcota. Macrolides were significantly correlated with microbial community composition changes in soil samples, while sulfonamides were significantly correlated with microbial community composition changes in root samples. Soil properties (total carbon and nitrogen contents and pH) influenced the shifts in microbial communities in rhizosphere soils and roots. This study provides evidence that low residual antibiotic levels in vegetable farms can shift microbial community structures, potentially affecting agroecosystem stability. However, the degree to which the shift occurs could be regulated by environmental factors, such as soil nutrient conditions.

Biocontrol Activity of Aromatic and Medicinal Plants and Their Bioactive Components against Soil-Borne Pathogens

Soil-borne phytopathogens can have detrimental effects on both cereal and horticultural crops resulting in serious losses worldwide. Due to their high efficiency and easy applicability, synthetic pesticides are still the primary choice in modern plant disease control systems, but stringent regulations and increasing environmental concerns make the search for sustainable alternatives more pressing than ever. In addition to the incorporation of botanicals into agricultural practices, the diversification of cropping systems with aromatic and medicinal plants is also an effective tool to control plant diseases through providing nutrients and shaping soil microbial communities. However, these techniques are not universally accepted and may negatively affect soil fertility if their application is not thoroughly controlled. Because the biocontrol potential of aromatic and medicinal plants has been extensively examined over the past decades, the present study aims to overview the recent literature concerning the biopesticide effect of secondary metabolites derived from aromatic and medicinal plants on important soil-borne plant pathogens including bacteria, fungi, and nematodes. Most of the investigated herbs belong to the family of Lamiaceae (e.g., Origanum spp., Salvia spp., Thymus spp., Mentha spp., etc.) and have been associated with potent antimicrobial activity, primarily due to their chemical constituents. The most frequently tested organisms include fungi, such as Rhizoctonia spp., Fusarium spp., and Phytophthora spp., which may be highly persistent in soil. Despite the intense research efforts dedicated to the development of plant-based pesticides, only a few species of aromatic herbs are utilized for the production of commercial formulations due to inconsistent efficiency, lack of field verification, costs, and prolonged authorization requirements. However, recycling the wastes from aromatic and medicinal plant-utilizing industries may offer an economically feasible way to improve soil health and reduce environmental burdens at the same time. Overall, this review provides comprehensive knowledge on the efficiency of aromatic herb-based plant protection techniques, and it also highlights the importance of exploiting the residues generated by aromatic plant-utilizing sectors as part of agro-industrial processes.

Ecological insights into soil health according to the genomic traits and environment-wide associations of bacteria in agricultural soils

Soil microbiomes are sensitive to current and previous soil conditions, and bacterial 'bioindicators' of biological, physical, and chemical soil properties have considerable potential for soil health assessment. However, the lack of ecological or physiological information for most soil microorganisms limits our ability to interpret the associations of bioindicators and, thus, their utility for guiding management. We identified bioindicators of tillage intensity and twelve soil properties used to rate soil health using a 16S rRNA gene-based survey of farmland across North America. We then inferred the genomic traits of bioindicators and evaluated their environment-wide associations (EWAS) with respect to agricultural management practice, disturbance, and plant associations with 89 studies from agroecosystems. Most bioindicators were either positively correlated with biological properties (e.g., organic matter) or negatively correlated with physical and chemical properties. Higher soil health ratings corresponded with smaller genome size and higher coding density, while lower ratings corresponded with larger genomes and higher rrn copy number. Community-weighted genome size explained most variation in health ratings. EWAS linked prominent bioindicators with the impacts of environmental disturbances. Our findings provide ecological insights into bioindicators of soil properties relevant to soil health management, illustrating the tight coupling of microbiome and soil function.

Effects of Domestication on Plant-Microbiome Interactions

Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.

Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India

Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 × 10⁷ gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO₄^3-, SO₄^2- and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO₄^2- and NO₃^- reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO₄^3- and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO₃^- reduction to ammonium), and S (assimilatory SO₄^2- reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.

Long-term cultivation alter soil bacterial community in a forest-grassland transition zone

Changes in land use types can significantly affect soil porperties and microbial community composition in many areas. However, the underlying mechanism of shift in bacterial communities link to soil properties is still unclear. In this study, Illumina high-throughput sequencing was used to analyze the changes of soil bacterial communities in different land use types in a forest-grassland transition zone, North China. There are two different land use types: grassland (G) and cultivated land (CL). Meanwhile, cultivated land includes cultivated of 10 years (CL10) or 20 years (CL20). Compared with G, CL decreased soil pH, SOC and TN, and significantly increased soil EC, P and K, and soil properties varied significantly with different cultivation years. Grassland reclamation increases the diversity of bacterial communities, the relative abundance of Proteobacteria, Gemmatimonadetes and Bacteroidetes increased, while that of Actinobacteria, Acidobacteria, Rokubacteria and Verrucomicrobia decreased. However, the relative abundance of Proteobacteria decreased and the relative abundance of Chloroflexi and Nitrospirae increased with the increase of cultivated land years. Mantel test and RDA analysis showed that TP, AP, SOC and EC were the main factors affecting the diversity of composition of bacterial communities. In conclusion, soil properties and bacterial communities were significantly altered after long-term cultivation. This study provides data support for land use and grassland ecological protection in this region.

Dolit S, K. Khamis A, Abd-Aziz N, R. Azman N, A. Asli U. Regenerating Soil Microbiome: Balancing Microbial CO2 Sequestration and Emission

Soil microbiome plays a significant role in soil’s ecosystem for soils to be physically and biologically healthy. Soil health is fundamental for plant growth and crops productivity. In the introduction part, the roles and dynamics of the microbial community in soils, primarily in the cycle of soil organic carbon and CO2 release and absorption, are deliberated. Next, the impact of crop management practices and climate change on the soil carbon balance are described, as well as other issues related to soil degradation, such as unbalanced nutrient recycling and mineral weathering. In response to these issues, various approaches to soil regeneration have been developed in order to foster an efficient and active soil microbiome, thereby balancing the CO2 cycle and carbon sequestration in the soil ecosystem.

Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks

Fertilization is the main strategy to accelerate vegetation restoration and improve the rhizosphere microbial community in the northeast China. However, the responses of rhizosphere microbial community structure, specific microbial community and symbiotic pattern to manure fertilization in grassland (alfalfa only) are not well clear. In this study, the variation of bacterial community structures in R_Manure (extracted liquid of fermented cow manure), E_Manure (extracted residue of fermented cow manure), F_Manure (full fermented cow manure), and Control (without fermented cow manure) collected from the rhizosphere microbial community of alfalfa were analyzed by the application of an Illumina HiSeq high-throughput sequencing technique. A total of 62,862 microbial operational taxonomic units (OTUs) were detected and derived from 21 phyla of known bacteria. The dominant bacteria in the rhizosphere include Proteobacteria (70.20%), Acidobacteria (1.24%), Actinobacteria (2.11%), Bacteroidetes (6.15%), Firmicutes (4.21%), and Chlorofexi (2.13%) accounting for 86% of the dominant phyla in all treatments. At the genus level, the dominant genus include NB1-j, Lysobacter, Alphaproteobacteria, Subgroup_6, Actinomarinales, Saccharimonadales, Aneurinibacillus, MO-CFX2, SBR1031, Caldilineaceae, and so on with the average relative abundance (RA) of 1.76%, 1.52%, 1.30%, 1.24%, 1.61%, 2.39%, 1.36%, 1.42%, 1.27%, and 1.03%, respectively. Bacterial diversities and community structures were significantly differentiated by different treatments of fertilization. The results of community structure composition showed that R_Manure treatment significantly increased the population abundance of Firmicutes, Chlorofexi, and Patescibacteria by 34.32%, 6.85%, and 2.70%, and decreased the population abundance of Proteobacteria and Actinobacteria by 16.83% and 1.04%, respectively. In addition, it showed that all treatments significantly resulted in an increase or decrease at the genus level. R_Manure had the higher richness and diversity of the bacterial community, with the greatest topology attributes of the co-occurrence networks. Through the analysis of the molecular ecological network (MENA), the co-occurrence networks had a shorter average path distance and diameter in R_Manure than in others, implying more stability to environmental changes. Redundancy analysis (RDA) showed that the ratio of carbon and nitrogen (C/N) was the main factor affecting rhizosphere microbial community composition while driving distinct rhizosphere bacterial community and its co-occurrence networks. The R_Manure associated with more C/N had relatively complex microbial co-occurrence network with a large number of nodes and edges, while the microbial network of others associated with less C/N had fewer taxa with loose mutual interactions. These results suggested that organic fertilizer with high C/N can regulate the rhizosphere microorganism, while high C/N can determine bacterial community structures, specific bacterial taxa, and their relationships with the nodule size of alfalfa. These significant changes can be used to evaluate soil fertility and fertilizer management in the artificial grassland system, while the potential biological indicators of the rhizosphere microbial community will play an important role in future eco-agriculture.

Characterization of Microbial Communities and Naturally Occurring Radionuclides in Soilless Growth Media Amended with Different Concentrations of Biochar

Biochar, derived from the pyrolysis of plant materials has the potential to enhance plant growth in soilless media. Howevetar, little is known about the impact of biochar amendments to soilless growth media, microbial community composition, and fate of chemical constituents in the media. In this study, different concentrations of biochar were added to soilless media and microbial composition, and chemical constituents were analyzed using metagenomics and gamma spectroscopy techniques, respectively. Across treatments, carboxyl-C, phenolic-C, and aromatic-C were the main carbon sources that influenced microbial community composition. Flavobacterium (39.7%), was the predominantly bacteria genus, followed by Acidibacter (12.2%), Terrimonas (10.1%), Cytophaga (7.5%), Ferruginibacter (6.0%), Lacunisphaera (5.9%), Cellvibrio (5.8%), Opitutus (4.8%), Mucilaginibacter (4.0%) and Bryobacter (4.0%). Negative relationships were found between Cytophaga and 226Ra (r = −0.84, p = 0.0047), 40K (r = −0.82, p = 0.0069) and 137Cs (r = −0.93, p = 0.0002). Similarly, Mucilaginibacter was negatively correlated with 226Ra (r = −0.83, p = 0.0054) and 137Cs (r = −0.87, p = 0.0021). Overall, the data suggest that high % biochar amended samples have high radioactivity concentration levels. Some microorganisms have less presence in high radioactivity concentration levels.

Indictors of wetland health improve following small-scale ecological restoration on private land

Globally wetlands are imperilled and restoring these highly productive and biodiverse ecosystems is key to regaining their lost function and health. Much of the fertile, low-lying land that was historically wetland is now farmed, so privately-owned locations play critical roles in regaining space for wetlands. However, wetland restoration on private property is often small-scale and supported by minimal funding and expertise. Little is known about what these efforts achieve, and what contexts facilitate the greatest gains in wetland health. Using a paired plot design for 18 restored and 18 unrestored wetlands, we aimed to understand changes in wetland health following restoration on private property. We characterised plant and microbial communities and soil characteristics following wetland restoration and explored how environmental settings of restored wetlands related to the clustering of wetland health indicators. We found that all indicators of wetland health significantly increased following restoration except for the ratio of Gram negative to Gram positive bacteria. Restoration enhanced plant alpha and beta diversity, adding ~13 native plant species per plot. Soils in restored wetlands contained 20% more organic matter, and 25% more microbial biomass, which was driven by an increased abundance of fungi. Restoration reduced soil bulk density by 0.19 g^-1 cm³ and Olsen Phosphorus by 23%. These effects on soil physical characteristics and microbial communities were strongest in the wettest locations. Restored wetlands clustered into three main groups based on indicators of wetland health. Hydrological flow explained the clustering of wetlands, with riverine wetlands exhibiting greater indicators of recovery than depressional wetlands, suggesting that hydrological flow may influence post-restoration recovery. Overall, this study shows that small-scale wetland restoration on private land improved wetland health, providing evidence that it can be an effective use of marginal agricultural land.

A review on effective soil health bio-indicators for ecosystem restoration and sustainability

Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.

Assessment of biotoxicity of three types of landfilled foundry waste on the basis of dehydrogenase activity

The microbiological activity of three types of landfilled foundry wastes, i.e. biologically reclaimed foundry waste (BFW), foundry waste landfilled since the 1990s (LFW) and fresh foundry waste (FFW), was investigated. The wastes originated from a Polish iron and steel foundry which uses organic binders based on phenol-formaldehyde resins and mineral binders to casting production. The physical and chemical properties and dehydrogenase activity (DHA) were determined in the waste samples and local soils. In addition, a pot experiment was performed to determine the effect of the addition of FFW with no microbial activity on soils. Additional correlation analysis was conducted between DHA and other parameters. It was found that biologically reclaimed foundry waste (BFW) showed the highest microbial activity, similar to soils from garden allotments and agricultural fields. The DHA in LFW was about a half lower than BFW. On the other hand, FFW did not show any microbial activity. A pot experiment showed that increasing the percentage of foundry waste relative to soil had a negative effect on DHA, probably as a result of soil dilution rather than the inhibitory effect of contaminants. It was concluded that the optimum addition of FFW to soils is 10% wt, due to the highest value of DHA among the other variants.

Effects of Bacillus subtilis A-5 and its fermented γ-polyglutamic acid on the rhizosphere bacterial community of Chinese cabbage

Chemical fertilizer reduction combined with novel and green agricultural inputs has become an important practice to improve microecological health in agricultural production. Given the close linkages between rhizosphere processes and plant nutrition and productivity, understanding how fertilization impacts this critical zone is highly important for optimizing plant–soil interactions and crop fitness for agricultural sustainability. Here, by using a pot experimental system, we demonstrated that nitrogen fertilizer reduction and microbial agent application promoted plant fitness and altered the microbial community structure in the rhizosphere soil with the following treatments: no fertilization, CK; conventional chemical fertilizer, CF; 30% reduced nitrogen fertilizer, N; 30% reduced nitrogen fertilizer with pure γ-PGA, PGA; 30% reduced nitrogen fertilizer with Bacillus subtilis A-5, A5; 30% reduced nitrogen fertilizer with γ-PGA fermentation broth, FJY. The PGA, A5, and FJY treatments all significantly promoted crop growth, and the FJY treatment showed the strongest positive effect on Chinese cabbage yield (26,385.09 kg/hm²) (P < 0.05). Microbial agents affected the α diversity of the rhizosphere bacterial community; the addition of B. subtilis A-5 (A5 and FJY treatments) significantly affected rhizospheric bacterial community structure. Urease activity and soil pH were the key factors affecting bacterial community structure and composition. The FJY treatment seemed to influence the relative abundances of important bacterial taxa related to metabolite degradation, predation, and nitrogen cycling. This discovery provides insight into the mechanism underlying the effects of microbial agent inputs on rhizosphere microbial community assembly and highlights a promising direction for the manipulation of the rhizosphere microbiome to yield beneficial outcomes.

Microbial Fertilization Improves Soil Health When Compared to Chemical Fumigation in Sweet Lily

Lanzhou Lily(Lilium davidii) var. unicolor, which is also known as sweet lily in China, is used as a type of food. This lily is distributed in narrow regions, propagates asexually, cultivates perennially, and cultivates commonly in serious consecutive replant problems (CRPs). Soil fumigation is commonly used to control soil-borne disease to alleviate crops’ consecutive replant problems (CRPs). However, due to the improper fumigation application, it is common to cause chemical hazard to crops. In this study, we designed a two-factor experiment to explore the bacterial and fungal community structure and some specific microbial groups in the lily rhizosphere soil after chemical versus bacterial fertilizer treatments, by using a metagenomic analysis of the treated soils. The results showed that metham-sodium soil fumigation (SMF treatment) significantly decreased plant growth, as well as it significantly decreased both soil fungal diversity and abundance at the OTUs levels, while Special 8™ microbial fertilizer supplement (MF treatment) significantly improved plant growth and increased fungal diversity and abundance. Under FM treatment, Chao1 richness and Shannon’s diversity increased by 6.70% and 35.09% compared to CK (no treatment). However, the bacterial diversity and abundance were not significantly changed among these treatments. The fungal and bacterial community structure were different in all treatments. In SMF treatment, the pathogenic fungal species Fusarium oxysporum increased compared to CK, but it significantly decreased in MF treatment; in MF and MMF treatments, some beneficial bacteria groups such as the bacterial phylum Proteobacteria and its member genus Sphingomonas, as well as the fungal genus Mortierella, increased compared to CK and SFM treatments, but the harmful bacterial genera Gemmatimona was decreased, as well as the harmful fungal genus Cryptococcus. Thus, we concluded that under chemical fumigation conditions, both fungal diversity loss and overall microorganism reduction, which impair multiple ecosystem function, in conjunction with the increase of harmful fungal species such as Fusarium oxysporum, are causes for soil degradation. On the other hand, under microbial fertilizer supplement, it was the fungal diversity increase, as well as these beneficial microorganisms groups’ accumulation, together with those harmful groups’ depletion, played important roles in restoring and improving soil health that suffered from the chemical fumigant hazard. In addition, the bacterial phylum Proteobacteria and its member genus Sphingomonas are involved in soil health recovery and promotion. The results also emphasized that whether soil is chemically fumigated or not, beneficial microorganism supplementary is effective in ensuring soil productivity.

Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex

Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions.

Legacies at work: plant-soil-microbiome interactions underpinning agricultural sustainability

Agricultural intensification has had long-lasting negative legacies largely because of excessive inputs of agrochemicals (e.g., fertilizers) and simplification of cropping systems (e.g., continuous monocropping). Conventional agricultural management focuses on suppressing these negative legacies. However, there is now increasing attention for creating positive above- and belowground legacies through selecting crop species/genotypes, optimizing temporal and spatial crop combinations, improving nutrient inputs, developing intelligent fertilizers, and applying soil or microbiome inoculations. This can lead to enhanced yields and reduced pest and disease pressure in cropping systems, and can also mitigate greenhouse gas emissions and enhance carbon sequestration in soils. Strengthening positive legacies requires a deeper understanding of plant-soil-microbiome interactions and innovative crop, input, and soil management which can help to achieve agricultural sustainability.

Trace Element Contents in Petrol-Contaminated Soil Following the Application of Compost and Mineral Materials

The global use of petroleum hydrocarbons as raw materials and an energy source in industry results in serious environmental, health, and ecological problems. Consequently, there is growing interest in the development of technologies for the rehabilitation of contaminated areas. This study was undertaken in order to determine the effect of different phytostabilising materials (compost, bentonite, and CaO) on the trace element content in soil contaminated with unleaded petroleum 95 (0, 2.5, 5, and 10 cm³ kg⁻¹ of soil). The doses of petroleum applied to the soil were based on the previously conducted preliminary experiment. The highest petroleum dose (10 cm³ kg⁻¹ of soil) significantly reduced the chromium, zinc, and cobalt contents in the soil. Petroleum increased the cadmium, lead, nickel, and copper contents in the soil. The materials used for phytostabilisation (compost, bentonite, calcium oxide) had a significant effect on the trace element content in the soil. The application of mineral materials (bentonite and calcium oxide) was more effective than the application of compost, compared to the control series (without soil amendments) as they reduced the contents of cadmium, chromium, nickel, and cobalt in the soil to the greatest extent. The reduction effect of bentonite and calcium oxide on the content of these trace elements in the soil was stronger than compost.

Shifts in rhizosphere microbial communities in Oplopanax elatus Nakai are related to soil chemical properties under different growth conditions

Plant growth environment plays an important role in shaping soil microbial communities. To understand the response of soil rhizosphere microbial communities in Oplopanax elatus Nakai plant to a changed growth conditions from natural habitation to cultivation after transplant. Here, a comparative study of soil chemical properties and microbial community using high-throughput sequencing was conducted under cultivated conditions (CT) and natural conditions (WT), in Changbai Mountain, Northeast of China. The results showed that rhizosphere soil in CT had higher pH and lower content of soil organic matter (SOM) and available nitrogen compared to WT. These changes influenced rhizosphere soil microbial communities, resulting in higher soil bacterial and fungi richness and diversity in CT soil, and increased the relative abundance of bacterial phyla Acidobacteria, Chloroflexi, Gemmatimonadetes, Firmicutes and Patescibacteria, and the fungi phyla Mortierellomycota and Zoopagomycota, while decreased bacterial phyla Actinobacteria, WPS-2, Gemmatimonadetes, and Verrucomicrobia, and the fungi phyla Ascomycota, and Basidiomycota. Redundancy analysis analysis indicated soil pH and SOM were the primarily environmental drivers in shaping the rhizosphere soil microbial community in O. elatus under varied growth conditions. Therefore, more attention on soil nutrition management especially organic fertilizer inputs should be paid in O. elatus cultivation.

Determinants of Soil Bacterial Diversity in a Black Soil Region in a Large-Scale Area

Soils in black soil areas are high in organic matter and rich in nutrients. Soil microorganisms are particularly critical to cultivated land. The objective of this study was to explore the influencing factors of soil bacterial diversity under special regional conditions in a black soil region. In this study, the cultivated land in a black soil area was used as the study area and a random forest was used to map the bacterial abundance in the black soil area based on 1810 sample points. DbMEM analysis was used to quantify the spatial effect of the black soil area and to identify the influencing factors of soil bacterial abundance in the black soil area in combination with soil properties, terrain, and climate. Results of a variation division showed that broad (8.336%), AT (accumulated temperature, 5.520%), and pH (4.184%) were the main factors affecting soil bacterial diversity. The broad effect was more significant in the spatial effect, which may be related to the local landscape configuration. Overall, our research showed that the influencing factors of soil bacteria will be affected by regional characteristics.

Metagenomic insights into the microbial community structure and resistomes of a tropical agricultural soil persistently inundated with pesticide and animal manure use

Persistent use of pesticides and animal manure in agricultural soils inadvertently introduced heavy metals and antibiotic/antibiotic resistance genes (ARGs) into the soil with deleterious consequences. The microbiome and heavy metal and antibiotic resistome of a pesticide and animal manure inundated agricultural soil (SL6) obtained from a vegetable farm at Otte, Eiyenkorin, Kwara State, Nigeria, was deciphered via shotgun metagenomics and functional annotation of putative ORFs (open reading frames). Structural metagenomics of SL6 microbiome revealed 29 phyla, 49 classes, 94 orders, 183 families, 366 genera, 424 species, and 260 strains with the preponderance of the phyla Proteobacteria (40%) and Actinobacteria (36%), classes Actinobacteria (36%), Alphaproteobacteria (18%), and Gammaproteobacteria (17%), and genera Kocuria (16%), Sphingobacterium (11%), and Brevundimonas (10%), respectively. Heavy metal resistance genes annotation conducted using Biocide and Metal Resistance Gene Database (BacMet) revealed the detection of genes responsible for the uptake, transport, detoxification, efflux, and regulation of copper, cadmium, zinc, nickel, chromium, cobalt, selenium, tungsten, mercury, and several others. ARG annotation using the Antibiotic Resistance Gene-annotation (ARG-ANNOT) revealed ARGs for 11 antibiotic classes with the preponderance of β-lactamases, mobilized colistin resistance determinant (mcr-1), macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside resistance genes, among others. The persistent use of pesticide and animal manure is strongly believed to play a major role in the proliferation of heavy metal and antibiotic resistance genes in the soil. This study revealed that agricultural soils inundated with pesticide and animal manure use are potential hotspots for ARG spread and may accentuate the spread of multidrug resistant clinical pathogens.

Ammonia-oxidizing bacteria rather than ammonia-oxidizing archaea dominate nitrification in a nitrogen-fertilized calcareous soil

Microbe-driven nitrification is a key process that affects nitrogen (N) utilization by plants and N loss to the environment in agro-ecosystems. Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are important microorganisms that dominate the ammonia oxidation process (the first and rate-limiting step of nitrification). Calcareous soils are widely distributed, accounting for more than 30% of the Earth's land. However, the effects of long-term N fertilization on the potential nitrification rate (PNR) and on AOA and AOB in calcareous soils are poorly understood. In this study, we comprehensively assessed the effects of N application (applied at five rates as urea with 0, 73.5, 105, 136.5 and 250 kg N ha^-1 for 12 years) on soil chemical characteristics, PNR, N use efficiency (NUE) and the community characteristics of AOB and AOA in a calcareous soil. N application rate affected AOB beta diversity more than that of AOA. Compared to no N control, N application significantly decreased the relative abundance of Group I.1b clade A of AOA and Nitrosospira cluster 3a.2 of AOB, but increased Nitrosomonas cluster 7 of AOB. The relative abundance of Nitrosospira cluster 3a.2 of AOB was negatively correlated with PNR. A structural equation model showed a direct effect of N application rate on the content of soil organic matter and nitrate, the alpha and beta diversity of AOA and AOB. Nitrate and AOB beta diversity were the key factors affecting PNR. Overall, the alpha, beta diversity and community composition of AOB contribute more to PNR than AOA in calcareous soils with high organic matter content. Understanding the relationship between the characteristics of AOA and AOB in calcareous soils and PNR will help to improve NUE.

Spatial variability and delineation of management zones based on soil micronutrient status in apple orchard soils of Kashmir valley, India

Knowledge and up-scaling of status, availability, and distribution of soil micronutrients are hugely significant for enhancing crop productivity and profitability. However, regional database entailing spatial variability of key micronutrients for a major apple-producing region like the Kashmir Himalayan Region (KHR) is missing. We investigated 588 topsoil samples between 2016 and 2017 (to 30 cm depth) to estimate spatial variability of extractable Zn, Cu, Mn, and Fe; develop spatial maps; and delineate potential management zones (MZs) in apple orchards using geo-statistical methods. Soil sampling was performed post-harvest season. Principal component analysis and fuzzy c-mean clustering were performed to develop MZs. Results exhibited wide variation, with high coefficient of variation (%) for Mn and Cu (123.9 and 114.4, respectively) and low (71.6) and medium (104) variability for Fe and Zn. Mean concentrations followed the order: Fe > Mn > Cu > Zn, with deficiencies evident towards central and northern regions of the study area. The best-fitted model was exponential. The nugget/sill ratio values were 0.41, 0.08, 0.37, and 0.38 for Zn, Cu, Mn, and Fe, respectively, indicating strong spatial dependence for Cu and moderate dependence for Fe, Zn, and Mn. Correlations between elevation, slope, and soil pH with micronutrients were negative, whereas with soil organic carbon and electrical conductivity positive relationships were identified. Three principal components accounted for 67·18% data variance. Based on the fuzzy performance index and modified partition entropy, five MZs were delineated, which exhibited variations from each other. These MZs highlighted the need for specific supplemental provisions in increasing soil fertility and apple productivity.

Gone with the Wind: Microbial Communities Associated with Dust from Emissive Farmlands

Dust is a major vehicle for the dispersal of microorganisms across the globe. While much attention has been focused on microbial dispersal in dust plumes from major natural dust sources, very little is known about the fractionation processes that select for the "dust microbiome." The recent identification of highly emissive, agricultural land dust sources in South Africa has provided the opportunity to study the displacement of microbial communities through dust generation and transport. In this study, we aimed to document the microbial communities that are carried in the dust from one of South Africa's most emissive locations, and to investigate the selective factors that control the partitioning of microbial communities from soil to dust. For this purpose, dust samples were generated at different emission sources using a Portable In-Situ Wind Erosion Lab (PI-SWERL), and the taxonomic composition of the resulting microbiomes was compared with the source soils. Dust emission processes resulted in the clear fractionation of the soil bacterial community, where dust samples were significantly enriched in spore-forming taxa. Conversely, little fractionation was observed in the soil fungal communities, such that the dust fungal fingerprint could be used to identify the source soil. Dust microbiomes were also found to vary according to the emission source, suggesting that land use significantly affected the structure and fractionation of microbial communities transported in dust plumes. In addition, several potential biological allergens of fungal origin were detected in the dust microbiomes, highlighting the potential detrimental effects of dust plumes emitted in South Africa. This study represents the first description of the fractionation of microbial taxa occurring at the source of dust plumes and provides a direct link between land use and its impact on the dust microbiome.

Continental-Scale Paddy Soil Bacterial Community Structure, Function, and Biotic Interaction

Rice paddy soil-associated microbiota participate in biogeochemical processes that underpin rice yield and soil sustainability, yet continental-scale biogeographic patterns of paddy soil microbiota remain elusive. The soil bacteria of four typical Chinese rice-growing regions were characterized and compared to those of nonpaddy soils. The paddy soil bacteria were significantly less diverse, with unique taxonomic and functional composition, and harbored distinct cooccurrence network topology. Both stochastic and deterministic processes shaped soil bacteria assembly, but paddy samples exhibited a stronger deterministic signature than nonpaddy samples. Compared to other environmental factors, climatic factors such as mean monthly precipitation and mean annual temperature described most of the variance in soil bacterial community structure. Cooccurrence network analysis suggests that the continental biogeographic variance in bacterial community structure was described by the competition between two mutually exclusive bacterial modules in the community. Keystone taxa identified in network models (Anaerolineales, Ignavibacteriae, and Deltaproteobacteria) were more sensitive to changes in environmental factors, leading us to conclude that environmental factors may influence paddy soil bacterial communities via these keystone taxa. Characterizing the uniqueness of bacterial community patterns in paddy soil (compared to nonpaddy soils) at continental scales is central to improving crop productivity and resilience and to sustaining agricultural soils.

IMPORTANCE Rice fields provide food for over half of the world’s human population. The ecology of paddy soil microbiomes is shaped by human activities, which can have a profound impact on rice yield, greenhouse gas emissions, and soil health. Investigations of the soil bacteria in four typical Chinese rice-growing regions showed that (i) soil bacterial communities maintain highly modularized species-to-species network structures; (ii) community patterns were shaped by the balance of integrated stochastic and deterministic processes, in which homogenizing selection and dispersal limitation dominate; and (iii) deterministic processes and climatic and edaphic factors influence community patterns mainly by their impact on highly connected nodes (i.e., keystone taxa) in networks. Characterizing the unique ecology of bacterial community patterns in paddy soil at a continental scale may lead to improved crop productivity and resilience, as well as sustaining agricultural soils.

Co-occurrence of antimicrobial and metal resistance genes in pig feces and agricultural fields fertilized with slurry

Antimicrobial resistance constitutes a global challenge to public health. The common addition of Zn, Cu and other metals to animal feed and the widespread presence of metal ions in livestock and their receiving environments may be a factor that facilitates the proliferation of antimicrobial resistance via co-selection of antimicrobial resistance genes (ARGs) and metal resistance genes (MRGs). However, the extent of co-selection is not yet fully understood. In this study, we used a metagenomic approach to profile ARGs, MRGs and mobile genetic elements (MGEs) known to constitute potential ARG and MRG vectors of transmission, and we determined the concentration of metal ions to assess the interrelationships between the occurrence of ARGs, MRGs and metal concentrations in samples from pig farms in China. Samples analyzed included fresh pig feces, soils fertilized with treated slurry, and sediments from aquatic environments, where effluent from treated slurry was discharged. Resistance genes to tetracycline and zinc were the most commonly observed ARGs and MRGs for all three types of samples. Significant correlations were observed between the abundance of ARGs and MRGs, and between ARGs/MRGs and MGEs, and between metal and ARGs/MGEs as documented by Pearson's correlation analysis (r > 0.9, P < 0.001). Further network analysis revealed significant co-occurrence between specific ARGs and MRGs, between ARGs/MRGs and MGEs, and between specific metals (Zn, Cr, and Mn) and ARGs and MGEs. Collectively, our findings demonstrate a high level of co-occurrence of antimicrobial and metal resistance genes in slurry from pig farms and their surrounding environments. The results suggest that metals added to pig feed might facilitate co-selection of ARGs and MGEs in the pig production environments, thereby resulting in a bigger pool of mobile ARGs.