Soil Microbial Community Dynamics Research Articles

Impact of Biochar on Fusarium Wilt of Cotton and the Dynamics of Soil Microbial Community

The effects of biochar on leaf and soil-borne diseases of plants can be seen in addition to its ability to sequester carbon, improve soil quality, and enhance plant performance. However, the mechanisms by which soil-borne pathogens are suppressed and plant performance is enhanced are not well understood. The present work aims to comprehensively establish the links between biochar-induced changes in the richness of the rhizosphere microbial population, in association with the reduction of soil-borne Fusarium wilt disease (Fusarium oxysporum f. sp. vasinfectum), in cotton (Gossypium hirsutum), with improved plant performance. Biochar made from organic waste significantly decreased the colonization and survival of Fusarium in soil, raised the culture-able counts of numerous microbes with biocontrol potential (microorganisms that boost plant growth and development), and inhibited Fusarium wilt of cotton. The biochar amendment significantly enhanced the cotton plant development and physiological parameters such as chlorophyll content, etc. Overall, 9% organic waste biochar had shown a significant impact on cotton growth as compared to other treatments with or without biochar. Compared to the soil-only control, the disease index was considerably reduced in all biochar-amended treatments. In terms of the plant’s resistance to Fusarium wilt, biochar-induced increases in the level of overall chlorophyll content and biochemicals such as phenolics, flavonoids, etc. Additionally, cotton plants grown with a 9% biochar composition had considerably greater NPK levels than other treatments with or without biochar. The biochar addition resulted in increased counts of Pseudomonas spp., Actinomycetes spp., and Trichoderma spp., while Acidobacteriales, Rhodospirillales, and Frankiales were less when compared with an un-amended (without biochar) soil control. Thus, the composition of rhizosphere bacteria in the treatments with and without modified biochar was found to differ significantly.

Rotational Grazing Strategies Minimally Impact Soil Microbial Communities and Carbon Dynamics—A Texas Case Study

The goal of our study was to evaluate the long-term (>12 years) influence of stocking density and herd rotation frequency on plant and soil microbial community and carbon dynamics in three working ranches in Texas. One ranch utilized a high stocking density and high-frequency (HIGH) rotation where cattle were moved multiple times each day; the second ranch used a medium stocking density and rotation frequency (MED) where herds were moved every 2–3 weeks; and the third ranch used a low stocking density with continuous grazing (LOW). Neither plant nor microbial diversity measures differed between the ranches, but plant functional and microbial community compositions differentiated management strategies. The MED ranch was characterized by a plant community dominated by little bluestem (Schizachyrium scoparium) and had the greatest soil organic matter content (2.8%) and soil respiration rates compared to the LOW (SOM = 2.2%) and HIGH (SOM = 2.1%) ranches. The HIGH ranch had a relatively high abundance and diversity of forbs and introduced grasses, and the LOW ranch had an even mixture of tall, introduced, and cool-season grasses. All three ranches had relatively high levels of Gram-positive bacteria (>70%) with MED having a higher relative abundance of bacteria important for carbon cycling. Furthermore, network analyses suggest that soil microbial communities at all ranches were highly synergistic and exhibited well-defined ecological niches. Differences in soil properties between ranches tended to be minor and suggest that grazing strategies can differ without any substantial shifts in soil and microbial function.

Composition of soil bacterial communities associated with urban stormwater detention basins and their predicted functional roles in N cycle.

Stormwater detention basins serve as vital components in mitigating the adverse effects of urban runoff, and investigating the microbial dynamics within these systems is crucial for enhancing their performance and pollutant removal capabilities. The aim of this study was to examine and compare the soil bacterial communities in two stormwater detention basins located on the Edwards Aquifer in Bexar County, Texas, USA, and evaluate how soil physiochemical properties may affect them. Each basin soil was sampled in two different seasons at varying depths and the structure of microbial communities was examined using paired end Illumina sequencing using V3 and V4 region of 16S rRNA gene. PICRUSt2 was used to predict functional genes in the nitrogen cycle. In addition, soil physicochemical properties such as pH, carbon, nitrogen, and phosphorus and particle size were examined. A beta diversity analysis revealed that basins had distinctive microbial communities. Additionally, soil particle size, phosphorus and ammonia significantly correlated with some of the dominant phyla in the basins. Proteobacteria and Acidobacteria showed a positive correlation with the relative abundances of nitrogen-cycling genes, while Actinobacteria showed a negative correlation. This study evaluated the associations between soil physicochemical properties and microbial community dynamics in stormwater basins. The study also predicts the relative abundance of nitrogen cycling genes, suggesting shared functional traits within microbial communities. The findings have implications for understanding the potential role of microbial communities in nitrogen cycling processes and contribute to developing sustainable stormwater management strategies and protecting water quality in urban areas.

Unravelling the dynamics of soil microbial communities under the environmental selection and range shift process in afforestation ecosystems

The process of forest range shift not only affects the vegetation aboveground but also influences the dynamics of belowground microbial communities. To investigate the changes in soil under forest range shift, we examined the natural forest soil microbiome along with its corresponding physicochemical properties, as well as the afforestation of natural forest by seedlings and sowing. By utilizing natural forests and employing different afforestation methods, we simulated the three stages of forest range shift: the staging stage, regeneration, and colonization. We employed network analysis and phylogenetic assemblages to examine the structure of soil microbial communities during these three stages in a macro-environmental change context. Ordination and regression analyses were also used to explore the correlation between microorganisms, environmental factors, and changes in their niches. The findings revealed that different afforestation (range shift) types led to distinct microbial compositions. Seedling afforestation exhibited similarities to mature forests, suggesting a significant influence on below-ground microorganisms. In contrast, sowing-based afforestation resulted in small changes in soil microbes, indicating a legacy effect on grassland soils. The impact of the rhizosphere on microbial composition remained consistent across the three forest types. Overall, this study underscores the significance of forest range shift in shaping soil microbial communities and emphasizes the need to consider these dynamics in forest management and restoration endeavours.

Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes

Land-use change is highly dynamic globally and there is great uncertainty about the effects of land-use legacies on contemporary environmental performance. We used a chronosequence of urban grasslands (lawns) that were converted from agricultural and forested lands from 10 to over 130 years prior to determine if land-use legacy influences components of soil biodiversity and composition over time. We used historical aerial imagery to identify sites in Baltimore County, MD (USA) with agricultural versus forest land-use history. Soil samples were taken from these sites as well as from existing well-studied agricultural and forest sites used as historical references by the National Science Foundation Long-Term Ecological Research Baltimore Ecosystem Study program. We found that the microbiomes in lawns of agricultural origin were similar to those in agricultural reference sites, which suggests that the ecological parameters on lawns and reference agricultural systems are similar in how they influence soil microbial community dynamics. In contrast, lawns that were previously forest showed distinct shifts in soil bacterial composition upon recent conversion but reverted back in composition similar to forest soils as the lawns aged over decades. Soil fungal communities shifted after forested land was converted to lawns, but unlike bacterial communities, did not revert in composition over time. Our results show that components of bacterial biodiversity and composition are resistant to change in previously forested lawns despite urbanization processes. Therefore land-use legacy, depending on the prior use, is an important factor to consider when examining urban ecological homogenization.

Exploration of Soil Microbial Diversity and Community Structure along Mid-Subtropical Elevation Gradients in Southeast China

Climate change is altering the abundance and distributions of natural communities in mountainous ecosystems, but the variations of soil microbial communities and their driving factors along elevation gradients at high altitudinal mid-subtropical zones have received limited attention. Such information is needed for a comprehensive understanding of the ecosystem’s response to intensifying climate changes. In this study, using Illumina sequencing, we investigated the shift in soil microbial diversity and community composition at eight evergreen broadleaf forest sites, which ranged from a low of 550 to a high of 1038 m above sea level (m a.s.l.) on Wuyi Mountain in Southeast China. Significant (p < 0.05) differences were observed only in the community structure of bacteria and fungi between the low and high elevation levels of forests, but not in their alpha-diversity indices. Soil bacterial diversity was significantly correlated with plant Shannon index. Likewise, plant richness and diversity modified soil bacterial community structures along the two elevations and were the best predictors. Soil pH was the main edaphic factor driving the fungal diversity across elevations, whereas inconsistency in the fungal trophic mode did not allow the identification of a determinant factor for soil fungal community structure. The variations of the predominant fungal trophic guilds, such as the symbiotrophs and pathotrophs, along elevation gradients were due to the plant richness and diversity prevailing at the low and high elevation levels of forest sites. The findings of this study reveal the soil microbial community dynamics and the local regulators across elevations on Wuyi mountain.

Components of N-fixation system response to glyphosate are un-coupled in agroecosystems

Glyphosate, introduced 50 years ago, is one of the most widely used herbicides. There are lingering concerns over the potential environmental impacts of glyphosate, prompting many studies. Many of these studies have isolated specific types of glyphosate effects – such as on N-fixation rate, or microbial community dynamics – but have not examined how glyphosate effects behave in relationship to one another. In this study, we evaluated the effect of glyphosate on biological N-fixation, soil microbial community dynamics, and soil nifH gene quantity within four types of crop management systems. Our hypothesis was that if farm management mediates the effects of glyphosate, then the effects of glyphosate on different N-fixing components of crop management systems should have coordinated effects; when one component is impacted, the others should be as well. We measured % N derived from the atmosphere (Ndfa) in soybean as a proxy for fixation, the quantity of 16S rRNA marker genes, and the nifH gene in Near soil (soil attached to roots) and Far soil (soil unattached, but under root influence) samples. We determined the response of putative diazotrophs to glyphosate in the Near and Far soil using a combination of Quantitative-Polymerase Chain Reaction (QPCR) and 16S gene amplicon sequencing. The crop management systems included two under conventional management (NT is No-till and CT is Chisel till) and two under organic rotations (O3 is a 3-year rotation, and O6 is a 6-year rotation). We found that glyphosate led to changes in some components, but that these effects were likely governed by separate mechanisms and did not behave in a coordinated manner. Glyphosate caused a decrease in Ndfa under CT; the effect of glyphosate on Ndfa across systems was weakly negatively correlated to the amount of soil organic matter in the crop management systems. The 16S rRNA gene abundance was not affected by glyphosate. Glyphosate caused a 217 % increase in nifH gene abundance in the rhizosphere, but this effect was not affected by crop management system. Glyphosate treatment affected community composition only in the Near soil of O6. The assemblage of taxa that responded to glyphosate in each system differed and it is possible that dynamics in the population of 16S sequence variants is decoupled from the selective pressure of glyphosate treatment in soils.

Seasonal dynamics of microbial communities in rhizosphere and bulk soils of two temperate forests

Microbial communities play an important role in regulating soil carbon and nutrient cycling in forest ecosystems. Understanding the seasonal variations of soil microbial community diversity and composition in both rhizosphere and bulk soils is of great significance for further understanding the carbon and nutrient cycling in temperate forest ecosystems. Here we analyzed the seasonal dynamics of paired rhizosphere and bulk soil microbial community of two temperate forests (Betula platyphylla and Quercus wutaishanica) in Dongling Mountain, Beijing, using high-throughput sequencing based on the Illumina Hiseq 2500 platform. Compared with bacteria, the difference of soil fungal diversity among seasons of the two temperate forests was more significant. Moreover, season (spring, summer, autumn and winter) and habitat (rhizosphere vs. bulk soil) had significant interaction effects on the composition of soil microbial communities. Concurrent with the variations in the diversity and composition of soil bacterial and fungal communities, the potential function of these microbial communities also changed significantly among seasons. These results are helpful in understanding the seasonal dynamics of soil microbial communities and their potential functioning in temperate forest ecosystems.

Spatiotemporal evolution and assembly processes of ammonia-oxidizing prokaryotic communities in 1 000-year-old coastal reclaimed soils

Coastal marshes are transitional areas between terrestrial and aquatic ecosystems. They are sensitive to climate change and anthropogenic activities. In recent decades, the reclamation of coastal marshes has greatly increased, and its effects on microbial communities in coastal marshes have been studied with great interest. Most of these studies have explained the short-term spatiotemporal variation in soil microbial community dynamics. However, the impact of reclamation on the community composition and assembly processes of functional microbes (e.g., ammonia-oxidizing prokaryotes) is often ignored. In this study, using quantitative polymerase chain reaction and the Ion S5™ XL sequencing platform, we investigated the spatiotemporal dynamics, assembly processes, and diversity patterns of ammonia-oxidizing prokaryotes in 1 000-year-old reclaimed coastal salt marshes. The taxonomic and phylogenetic diversity and composition of ammonia oxidizers showed apparent spatiotemporal variations with soil reclamation. Phylogenetic null modelling-based analysis showed that across all sites, the archaeal ammonia-oxidizing community was assembled by a deterministic process (84.71%), and deterministic processes were also dominant (55.2%) for ammonia-oxidizing bacterial communities except for communities at 60 years of reclamation. The assembly process and nitrification activity in reclaimed soils were positively correlated. The abundance of the amoA gene and changes in ammonia-oxidizing archaeal and bacterial diversities significantly affected the nitrification activity in reclaimed soils. These findings suggest that long-term coastal salt marsh reclamation affects nitrification by modulating the activities of ammonia-oxidizing microorganisms and regulating their community structures and assembly processes. These results provide a better understanding of the effects of long-term land reclamation on soil nitrogen-cycling microbial communities.

Short- and long-term effects of continuous compost amendment on soil microbiome community

Organic amendment, and especially the use of composts, is a well-accepted sustainable agricultural practice. Compost increases soil carbon and microbial biomass, changes enzymatic activity, and enriches soil carbon and nitrogen stocks. However, relatively little is known about the immediate and long-term temporal dynamics of agricultural soil microbial communities following repeated compost applications. Our study was conducted at two field sites: Newe Ya'ar (NY, Mediterranean climate) and Gilat (G, semi-arid climate), both managed organically over 4 years under either conventional fertilization (0, zero compost) or three levels of compost amendment (20, 40 and 60 m3/ha or 2, 4, 6 L/m2). Microbial community dynamics in the soils was examined by high- and low-time-resolution analyses. Annual community composition in compost-amended soils was significantly affected by compost amendment levels in G (first, second and third years) and in NY (third year). Repeated sampling at high resolution (9–10 times over 1 year) showed that at both sites, compost application initially induced a strong shift in microbial communities, lasting for up to 1 month, followed by a milder response. Compost application significantly elevated alpha diversity at both sites, but differed in the compost–dose correlation effect. We demonstrate higher abundance of taxa putatively involved in organic decomposition and characterized compost-related indicator taxa and a compost-derived core microbiome at both sites. Overall, this study describes temporal changes in the ecology of soil microbiomes in response to compost vs. conventional fertilization.

Changes in soil bacterial community along a gradient of permafrost degradation in Northeast China

Spatial fragmentation of permafrost alters soil hydrothermal conditions and physicochemical properties that control microbial activity responsible for the decomposition of organic matter. Due to climate warming, there is a need to identify changes in microbial community and diversity to predict altered soil function along permafrost degradation gradient. To determine the drivers of soil bacterial community at regional (across permafrost regions) and local scales (across habitats, within permafrost region), the method of “space instead of time” was adopted. The soil samples were collected from forest and wetland ecosystems in three types of west-east permafrost regions (including discontinuous, sporadic and isolated patches permafrost regions, which represent the primary degenerate sequence) in Northeast China. The results showed that Chloroflexi, Proteobacteria, Actinobacteria, and Acidobacteria were the most abundant phyla. The effect of permafrost degradation on bacterial relative abundance varied by species and habitats. The response of soil bacterial α-diversity (the observed OTU richness and phylogenetic diversity) in forests and wetlands to permafrost degradation were inconsistent. It was significantly correlated with mean annual temperature (MAT), mean annual precipitation (MAP), soil pH, soil microbial biomass carbon (MBC) and nitrogen (MBN) contents. The structure of soil bacterial community became increasingly dissimilar with degradation, indicating that permafrost degradation significantly changed the bacterial community structure. Climate conditions and edaphic factors jointly contribute to 92 % of the variance in the soil bacterial diversity and 40 % in community composition. The results are valuable for understanding the dynamics of soil microbial community and potential carbon feedback to future climate warming in permafrost regions.

Dynamic analysis of the microbial communities and metabolome of healthy banana rhizosphere soil during one growth cycle.

The banana-growing rhizosphere soil ecosystem is very complex and consists of an entangled network of interactions between banana plants, microbes and soil, so identifying key components in banana production is difficult. Most of the previous studies on these interactions ignore the role of the banana plant. At present, there is no research on the the micro-ecological environment of the banana planting growth cycle. Based on high-throughput sequencing technology and metabolomics technology, this study analyzed the rhizosphere soil microbial community and metabolic dynamics of healthy banana plants during one growth cycle. Assessing the microbial community composition of healthy banana rhizosphere soil, we found that the bacteria with the highest levels were Proteobacteria, Chloroflexi, and Acidobacteria, and the dominant fungi were Ascomycota, Basidiomycota, and Mortierellomycota. The metabolite profile of healthy banana rhizosphere soil showed that sugars, lipids and organic acids were the most abundant, accounting for about 50% of the total metabolites. The correlation network between fungi and metabolites was more complex than that of bacteria and metabolites. In a soil environment with acidic pH, bacterial genera showed a significant negative correlation with pH value, while fungal genera showed no significant negative correlation with pH value. The network interactions between bacteria, between fungi, and between bacteria and fungi were all positively correlated. Healthy banana rhizosphere soil not only has a stable micro-ecology, but also has stable metabolic characteristics. The microorganisms in healthy banana rhizosphere soil have mutually beneficial rather than competitive relationships.

A less complex but more specialized microbial network resulted in faster fine-root decomposition in young stands of Robinia pseudoacacia

Microorganisms play an important role in litter decomposition. Bacteria and fungi colonize litter during the decomposition process; therefore, understanding the interactions of bacterial and fungal communities can yield insight into litter decomposition dynamics. Most studies have focused on leaf litter decomposition, but thus far, there has been little information on the dynamic changes in soil microbial composition at the different stages of fine-root decomposition. Therefore, we conducted a 210-day incubation experiment on the fine roots of Robinia pseudoacacia to explore how the temporal dynamics of soil enzyme activities and microbial communities are related to the decomposition of R. pseudoacacia at four different stand ages (15, 25, 35 and 45 years) during vegetation restoration. The results showed that the fine-root decomposition rate was higher for young stands of R. pseudoacacia. We found that the oxidase activity was significantly higher in the young stands (15 and 25 years) than in the old stands (35 and 45 years), while the hydrolase activity showed the opposite trend. The main reason for the higher decomposition rate in young stands of R. pseudoacacia was the high oxidase enzyme activities and less complex but more specialized microbial network of younger stands. The occurrence network was used to identify the keystone taxa by statistical analysis, and the key taxa changed from Acidobacteria to Proteobacteria during vegetation restoration. These findings demonstrate that vegetation restoration alters the soil microorganism community and network structure during fine-root decomposition of R. pseudoacacia. This finding is of great significance for understanding the role of microorganisms in regulating fine-root decomposition dynamics.

Soil biogeochemistry and microbial community dynamics in Pinus pinaster Ait. forests subjected to increased fire frequency

Fire frequency might increase in many fire-dominated ecosystems of the world due to the combined effects of global warming, land-use change and increased human pressures. Understanding how changes in fire frequency can affect the main soil biogeochemical dynamics, as well as the microbial community, in the long term is utmost important. Here we determined the effect of changes in fire frequency and other fire history characteristics on soil C and N dynamics and the main microbial groups (using soil fatty acid profiles), in Pinus pinaster forests from central Spain. Stands were chosen to differ in the number of fires (1 to 3) occurred between 1976 and 2018, in the time elapsed since the last fire and the interval undergone between the last two consecutive fires. We found that, in general, most of the studied biogeochemical and microbial variables showed clear differences between unburned and burned stands. The time elapsed since the last fire was the most important fire history covariable and governed the main soil nutrient dynamics and microbial groups. Recovery to pre-fire values took 30–40 years. Increased wildfire frequency only modified total C and nitrification rate, but results were not consistent between stands burned twice and thrice. The time interval (years) between the last two fires was not a significant covariable. The fact that some stands burnt up to thrice in a period of 43 years supports the strong capacity of this ecosystem to recover, even under an increased fire frequency.

Mixed grass species differ in rhizosphere microbial community structure and function response to drought compared to monocultures

Natural grassland succession is the interactions among different grass species and various environmental factors. The dynamics of soil microbial communities along succession stages has received tremendous attention. The effects of the coexistence of different grass species on the structure and function of rhizosphere soil microbial communities, however, are poorly understood, especially under drought stress conditions. Here, we investigated how different grass planting patterns and soil water content affect rhizosphere microbial community structure and function. Two typical grass species (Bothriochloa ischaemum and Stipa bungeana) on the Loess Plateau were planted in three planting systems: B. ischaemum monoculture, S. bungeana monoculture, and a mixed culture of the two species under two water regimes (optimal water: 80% field capacity [FC]; drought stress: 60% FC). Rhizosphere soil samples were collected to evaluate the rhizosphere microbial community structure (via phospholipid fatty acid [PLFA] biomarkers) and function (via six enzyme activities). The mixed culture of grass species noticeably shifted the rhizosphere microbial community structure. It caused the rhizosphere gram-positive:gram-negative PLFA ratio and fungal:bacterial PLFA ratio to increase under optimum water conditions. In comparison, drought stress caused total PLFA, bacterial PLFA, and gram-positive PLFA biomass to increase. Drought stress caused rhizosphere-specific enzyme activity to increase under monoculture treatment and rhizosphere-specific enzyme activity to decrease under mixed culture treatment. Soil water-soluble organic carbon, pH, and water-soluble organic phosphorus were the most important factors driving changes to rhizosphere microbial community composition. In comparison, pH was the predominant factor driving variation in rhizosphere specific enzyme activities. Thus, the coexistence of grass species altered the structure and function of the rhizosphere microbial community through changes in rhizosphere pH and water-soluble nutrients. In conclusion, changes to rhizodeposits under a mixed culture of grass species likely affect the structure and function of the rhizosphere microbial community. The results of the present study improve our understanding of the impacts of grass species interaction on soil biogeochemical processes under future global drought stress scenarios.

Climate warming restructures seasonal dynamics of grassland soil microbial communities.

Soil microbial community's responses to climate warming alter the global carbon cycle. In temperate ecosystems, soil microbial communities function along seasonal cycles. However, little is known about how the responses of soil microbial communities to warming vary when the season changes. In this study, we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall-grass prairie ecosystem. Our results showed that warming significantly (p = 0.001) shifted community structure, such that the differences of microbial communities between warming and control plots increased nonlinearly (R 2 = 0.578, p = 0.021) from spring to winter. Also, warming significantly (p < 0.050) increased microbial network complexity and robustness, especially during the colder seasons, despite large variations in network size and complexity in different seasons. In addition, the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer. Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem. Such seasonality of microbial responses to warming may enlarge over time and could have significant impacts on theterrestrial carbon cycle.

Groundwater depth regulates assembly processes of abundant and rare bacterial communities across arid inland river basin

Although numerous studies on bacterial biogeographic patterns in dryland have been conducted, bacterial community assembly across arid inland river basins is unclear. Here, we assessed the ecological drivers that regulate the assembly processes of abundant (ABS) and rare (RBS) bacterial subcommunities based on 162 soil samples collected in an arid inland river basin of China. The results showed that: (1) ABS exhibited a steeper distance–decay slope, and were more strongly affected by dispersal limitation (75.5% and 84.5%), than RBS in surface and subsurface soil. RBS were predominantly controlled by variable selection (54.6% and 50.2%). (2) Soil electric conductivity played a decisive role in mediating the balance between deterministic and stochastic processes of ABS and RBS in surface soil, increasing soil electric conductivity increased the importance of deterministic process. For subsurface soil, soil available phosphorus (SAP) and soil pH drove the balance in the assembly processes of ABS and RBS, respectively. The RBS shifted from determinism to stochasticity with decreased pH, while the dominance of deterministic processes was higher in low-SAP sites. (3) Groundwater depth seasonality had substantial effects on the assembly processes of ABS and RBS, but groundwater depth seasonality affected them indirectly mainly by regulating soil properties. Collectively, our study provides robust evidence that groundwater-driven variations in soil properties mediates the community assembly process of soil bacteria in arid inland river basins. This finding is of importance for forecasting the dynamics of soil microbial community and soil process in response to current and future depleted groundwater.

Soil microbial community dynamics during ryegrass green manuring and brassica biofumigation

The use of green manure and biofumigant crops within cropping rotations is a common practice for increasing soil fertility, organic carbon levels, improving soil aggregation and preventing erosion. These practices aim to increase the resilience of agricultural soils to degradation and protect important ecosystem services. However, knowledge of how soil microbial communities respond to biofumigation and green manuring at fine time scales is lacking, and this information is required to determine when organic amendments produce their maximum effect and how long their effects last.This study compared how a winter-grown ryegrass green manure (Lolium multiflorum, var. Tetila) and brassica biofumigant (Brassica juncea, var. Caliente 199) affected the bacterial, fungal and non-fungal eukaryote communities of an intensively cropped temperate vegetable production soil. The aim was to determine the timing, magnitude and duration of ryegrass green manuring and brassica biofumigation's effects on the microbial community dynamics of the bulk soil. We analysed the soil microbial communities with high throughput amplicon sequencing of soil DNA extracts at key times within one growing season, focussing on the period around incorporation, to determine how the communities changed in response to the treatments.Ryegrass and biofumigant green manure crops both had significant effects on the soil microbial ecosystem, and the fungal and non-fungal eukaryote communities were more responsive than the bacteria. Community change in the biofumigant and ryegrass treated plots was greatest in the weeks immediately after incorporation and slowly receded with time. However, the fungal and non-fungal eukaryote communities of all treatments remained significantly different to each other at the end of the experiment 35 weeks post-incorporation. We also found that soil pH was variable across the site and strongly related to differences in bacterial, fungal and eukaryote community structure.

Succession of soil bacterial communities and network patterns in response to conventional and biodegradable microplastics: A microcosmic study in Mollisol

Significant soil contamination of microplastics (MPs) by the application of agricultural mulching films has aroused global concern, however, the effects of conventional and biodegradable MPs on the dynamics of soil microbial communities and network patterns have not been sufficiently reported. In this study, we conducted a soil microcosmic experiment by adding low-density polyethylene and biodegradable MPs (PE and BD) into a black soil at the dosages of 0 % (CK), 0.1 % (low-dose, w/w), 1 % (medium-dose, w/w) and 5 % (high-dose, w/w), and soils were sampled on the 15th, 30th, 60th and 90th day of soil incubation for high-throughput sequencing. The results showed that the incubation time was the most influential factor driving the variations in bacterial community structures, and significant effects of MP dosages and types were also detected. With the increase in MP dosage, bacterial diversity markedly increased and decreased at the beginning (D15) and end of sampling day (D90), respectively. Compared to CK, BD induced a larger community dissimilarity than PE and tended to enrich environmentally friendly taxa, while PE likely promoted the growth of hazardous taxa. Moreover, BD simplified interspecies interactions compared to the networks of PE and CK, and Nitrospira was identified as a keystone species in both PE and BD networks. These findings provide new insights into the influences of conventional and biodegradable MPs on the succession patterns of soil bacterial communities, and further studies are needed to explore the soil metabolic potentials affected by the presence of MPs.

Composition, Structure and Diversity of Soil Bacterial Communities before, during and after Transit through the Gut of the Earthworm Aporrectodea caliginosa.

Earthworms heavily modify the soil microbiome as it passes throughout their guts. However, there are no detailed studies describing changes in the composition, structure and diversity of soil microbiomes during gut transit and once they are released back to the soil as casts. To address this knowledge gap, we used 16S rRNA next-generation sequencing to characterize the microbiomes of soil, gut and casts from the earthworm Aporrectodea caliginosa. We also studied whether these three microbiomes are clearly distinct in composition or can be merged into metacommunities. A large proportion of bacteria was unique to each microbiome—soil (82%), gut (89%) and casts (75%), which indicates that the soil microbiome is greatly modified during gut transit. The three microbiomes also differed in alpha diversity, which peaked during gut transit and decreased in casts. Furthermore, gut transit also modified the structure of the soil microbiome, which clustered away from those of the earthworm gut and cast samples. However, this clustering pattern was not supported by metacommunity analysis, which indicated that soil and gut samples make up one metacommunity and cast samples another. These results have important implications for understanding the dynamics of soil microbial communities and nutrient cycles.