Bulk Soil Microbial Community Research Articles

The Immediate Hotspot of Microbial Nitrogen Cycling in an Oil-Seed Rape (Brassica campestris L.) Soil System Is the Bulk Soil Rather Than the Rhizosphere after Biofertilization.

Biofertilizers are substances that promote plant growth through the efficacy of living microorganisms. The functional microbes comprising biofertilizers are effective mediators in plant-soil systems in the regulation of nitrogen cycling, especially in nitrification repression. However, the deterministic or stochastic distribution of the functional hotspot where microbes are active immediately after biofertilization is rarely investigated. Here, pot experiments with oil-seed rape (Brassica campestris L.) were conducted with various chemical and biological fertilizers in order to reveal the distribution of the hotspot after each fertilization. A stimulated dynamic of the nitrogen cycling-related genes in the bulk soil inferred that the bulk soil was likely to be the hotspot where the inoculated bacterial fertilizers dominated the nitrogen cycle. Furthermore, a network analysis showed that bulk soil microbial communities were more cooperative than those in the rhizosphere after biofertilization, suggesting that the microbiome of the bulk soils were more efficient for nutrient cycling. In addition, the relatively abundant ammonia-oxidizing bacteria and archaea present in the networks of bulk soil microbial communities further indicated that the bulk soil was the plausible hotspot after the application of the biofertilizers. Therefore, our research provides a new insight into the explicit practice of plant fertilization and agricultural management, which may improve the implementational efficiency of biofertilization.

Intercropping Systems Modify Desert Plant-Associated Microbial Communities and Weaken Host Effects in a Hyper-Arid Desert.

Intercropping is an important practice in promoting plant diversity and productivity. Compared to the accumulated understanding of the legume/non-legume crop intercrops, very little is known about the effect of this practice when applied to native species on soil microbial communities in the desert ecosystem. Therefore, in the present study, bulk soil and rhizosphere microbial communities in the 2-year Alhagi sparsifolia (legume)/Karelinia caspica (non-legume) monoculture vs. intercropping systems were characterized under field conditions. Our result revealed that plant species identities caused a significant effect on microbial community composition in monocultures but not in intercropping systems. Monoculture weakened the rhizosphere effect on fungal richness. The composition of bacterial and fungal communities (β-diversity) was significantly modified by intercropping, while bacterial richness (Chao1) was comparable between the two planting patterns. Network analysis revealed that Actinobacteria, α- and γ-proteobacteria dominated bulk soil and rhizosphere microbial co-occurrence networks in each planting pattern. Intercropping systems induced a more complex rhizosphere microbial community and a more modular and stable bulk soil microbial network. Keystone taxa prevailed in intercropping systems and were Actinobacteria-dominated. Overall, planting patterns and soil compartments, not plant identities, differentiated root-associated microbiomes. Intercropping can modify the co-occurrence patterns of bulk soil and rhizosphere microorganisms in desert ecosystems. These findings provided a potential strategy for us to manipulate desert soil microbial communities and optimize desert species allocation in vegetation sustainability.

Tuberosphere and bulk soil microbial communities in fields differing in common scab severity are distinguished by soil chemistry and interactions with pathogens

Tuberosphere and bulk soil microbial communities in fields differing in common scab severity are distinguished by soil chemistry and interactions with pathogens

Artificial Plantation Responses to Periodic Submergence in Massive Dam and Reservoir Riparian Zones: Changes in Soil Properties and Bacterial Community Characteristics.

Simple SummaryThis study focuses on plants in riparian zones that are very vulnerable due to water stress and anthropogenic disturbances, which are particularly important regarding their ecological and environmental role. Although plants and microbiome interactions are necessary for plant nutrient acquisition, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities of different artificial vegetation types in riparian areas of massive dams and reservoirs. Therefore, this study aims to assess the responses of woody and herbaceous plants in the riparian zones of the Three Gorges Dam Reservoir, China. Results revealed that the weight of dominant soil bacteria in different periods, including Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Cyanobacteria, was higher, and their composition was different in the rhizosphere, bulk soil, and endophyte. In the soil co-occurrence networks, the weight of soil physical properties was higher than chemical properties in the early emergence stage. The current study provides knowledge about bacteria in bulk, rhizosphere soils, and within roots in different emergence phases. Additionally, these results provide valuable information to inoculate the soil with key microbiota members by applying fertilizers, potentially improving plant and soil production and health.Plant and microbiome interactions are necessary for plant nutrient acquisition. However, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities in different artificial vegetation types (woody and herbaceous) in riparian areas of massive dams and reservoirs. Therefore, this study aims to assess such responses at elevations of 165–170 m a.s.l. in the riparian zones of the Three Gorges Dam Reservoir, China. The samples were collected containing the rhizosphere soil, bulk soil, and roots of herbaceous and woody vegetation at different emergence stages in 2018. Then, all the samples were analyzed to quantify the soil properties, bacterial community characteristics, and their interaction in the early and late emergence phases. In different periods, the weight of dominant soil bacteria, including Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Cyanobacteria, was higher, and their composition was different in the rhizosphere, bulk soil, and endophytes. Moreover, the soil co-occurrence networks indicated that the weight of soil physical properties was higher than chemical properties in the early emergence stage. In contrast, the weight of chemical properties was relatively higher in the late emergence stage. Furthermore, the richness and diversity of the bacterial community were mainly affected by soil organic matter. This study suggests that these herbaceous and woody vegetation are suitable for planting in reservoir areas affected by hydrology and human disturbance in light of soil nutrients and soil microbial communities, respectively. Additionally, these results provide valuable information to inoculate the soil with key microbiota members by applying fertilizers, potentially improving plant health and soil production.

Effects of Microbial Consortia, Applied as Fertilizer Coating, on Soil and Rhizosphere Microbial Communities and Potato Yield

The use of biological inputs in crop production systems, as complements to synthetic inputs, is gaining popularity in the agricultural industry due to increasing consumer demand for more environmentally friendly agriculture. An approach to meeting this demand is the inoculation of field crops with beneficial microbes to promote plant growth and resistance to biotic and abiotic stresses. However, the scientific literature reports inconsistent results following applications of bio-inoculant to fields. The effects of inoculation with beneficial microbes on bulk soil and rhizospheric microbial communities is often overlooked as precise monitoring of soil microbial communities is difficult. The aim of this research was to use Illumina high throughput sequencing (HTS) to shed light on bulk soil and rhizospheric microbial community responses to two commercial microbial inoculants coated onto fertilizer granules, applied to potato fields. Bulk soil samples were collected 4 days before seeding (May 27th), 7 days after seeding (June 7th), at potato shoot emergence (June 21st) and at mid-flowering (July 26th). Rhizospheric soil was collected at the mid-flowering stage. The Illumina MiSeq HTS results indicated that the bulk soil microbial community composition, especially prokaryotes, changed significantly across potato growth stages. Microbial inoculation did not affect bulk soil or rhizospheric microbial communities sampled at the mid-flowering stage. However, a detailed analysis of the HTS results showed that bulk soil and rhizospheric microbial community richness and composition were different for the first treatment block compared to the other three blocks. The spatial heterogeneity of the soil microbial community between blocks of plots was associated with potato tuber yield changes, indicating links between crop productivity and soil microbial community composition. Understanding these links could help in production of high-quality microbial inoculants to promote potato productivity.

Drivers of soil microbial community assembly during recovery from selective logging and clear‐cutting

Abstract Despite important progress in understanding the impacts of forest clearing and logging on above‐ground communities, how these disturbances affect soil microbial β‐diversity and the ecological processes driving microbial assemblages are poorly understood. Furthermore, whether and how the microbial shifts affect vegetation composition and diversity during recovery of post‐logged forests remain elusive. Using a spatial grid experiment design in a primary tropical forest intermixed with post‐logged patches naturally recovered for half century in Hainan Island, China, we characterized and explained the distance–decay relationships of soil microbial similarities in primary, selectively logged and clear‐cut forests. Selectively logged sites showed a lower spatial turnover rate of bacterial assemblages based on phylogenetic and taxonomic β‐diversity, but a higher spatial turnover rate of fungal assemblages based on phylogenetic β‐diversity, suggesting a higher level of phylogenetic variability in fungal composition. Clear‐cut sites showed lower spatial turnover for both bacterial and fungal assemblages based on the two β‐diversity, indicating community homogenization. Main drivers of microbial assemblages shifted from soil properties in primary forest to tree composition in selectively logged sites, whereas microbial–tree associations declined in clear‐cut sites, leading to stochastically organized microbial assemblages. Synthesis and applications. The increased fungal phylogenetic turnover with tree turnover following selective logging promotes unassisted recovery of plant diversity. In contrast, the decoupling of tree and microbial turnover following clear‐cutting suggests restoration approaches based on tree planting, and tree species that have strong associations with bulk soil microbial community should be considered. Our findings advance the understanding of spatial patterns, processes and drivers of soil microbial assemblages in parallel with tree community recovery during regeneration of post‐logged tropical forests, and highlight the importance of coupling assemblage patterns between tree and soil fungal communities for conserving tropical forest biodiversity.

Temporal Soil Bacterial Community Responses to Cropping Systems and Crop Identity in Dryland Agroecosystems of the Northern Great Plains

Industrialized agriculture results in simplified landscapes where many of the regulatory ecosystem functions driven by soil biological and physicochemical characteristics have been hampered or replaced with intensive, synthetic inputs. To restore long-term agricultural sustainability and soil health, soil should function as both a resource and a complex ecosystem. In this study, we examined how cropping systems impact soil bacterial community diversity and composition, important indicators of soil ecosystem health. Soils from a representative cropping system in the semi-arid Northern Great Plains were collected in June and August of 2017 from the final phase of a 5-year crop rotation managed either with chemical inputs and no-tillage, as a USDA-certified organic tillage system, or as a USDA-certified organic sheep grazing system with reduced tillage intensity. DNA was extracted and sequenced for bacteria community analysis via 16S rRNA gene sequencing. Bacterial richness and diversity decreased in all farming systems from June to August and was lowest in the chemical no-tillage system, while evenness increased over the sampling period. Crop species identity did not affect bacterial richness, diversity, or evenness. Conventional no-till, organic tilled, and organic grazed management systems resulted in dissimilar microbial communities. Overall, cropping systems and seasonal changes had a greater effect on microbial community structure and diversity than crop identity. Future research should assess how the rhizobiome responds to the specific phases of a crop rotation, as differences in bulk soil microbial communities by crop identity were not detectable.

Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem.

Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

Impact of long-term fertilizer and summer warming treatments on bulk soil and birch rhizosphere microbial communities in mesic arctic tundra

ABSTRACT Recent climate warming in the Arctic is enhancing microbial decomposition of soil organic matter, which may result in globally significant greenhouse gas releases to the atmosphere. To better predict future impacts, bacterial and fungal community structures in both the bulk soil and the rhizosphere of Arctic birch, Betula glandulosa, were determined in control, greenhouse summer warming, and annual factorial nitrogen (N) and phosphate (P) addition treatments twelve years after their establishment. DNA sequence analyses at multiple taxonomic levels consistently indicated substantial bulk soil and rhizosphere microbial community differences among the fertilization treatments but no significant greenhouse effects. These results suggest that climate warming will likely increase the activity rates of soil microbial decomposers but without substantially altering the structure of either the bacterial or fungal communities. Differential abundance testing revealed changes in ectomycorrhizal fungal species of the genus Thelephora in both bulk soil and rhizosphere, with increases in their relative abundance in P and N + P amended plots compared with warming and controls. Because birch is the principal low Arctic ectomycorrhizal host, our results suggest that these fungi may promote this shrub’s competitiveness where tundra soil nutrient availability is enhanced by warming or other means, ultimately contributing to arctic vegetation “greening.”

Niche width of above- and below-ground organisms varied in predicting biodiversity profiling along a latitudinal gradient.

Biodiversity is the foundation of all ecosystems across the planet, and having a better understanding of its global distribution mechanism could be important for biodiversity conservation under global change. A niche width model, combined with metabolic theory, has successfully predicted the increase of α-diversity and decrease of β-diversity in the below-ground microbial community along an altitudinal mountain gradient. In this study, we evaluated this niche width model of above-ground plants (mainly trees and shrubs) and below-ground bulk soil microbial communities (i.e., bacteria and archaea) along a latitudinal gradient of forests in China. The niche widths of both plants and microbes increased with increasing temperature and precipitation, and with proximity to circumneutral pH. However, the α- and β-diversities (observed richness and Bray-Curtis dissimilarity, respectively) could not be accurately predicted by a single niche width model alone, either temperature, precipitation or pH. Considering the interactions among different niche width models, all three niche width models were combined to predict biodiversity at the community level using structural equation modelling. The results showed that the niche width model of circumneutral pH was most important in predicting diversity profiling (i.e., α- and β-diversity) for both plants and microbes, while niche width of precipitation and temperature showed both direct and indirect importance for microbe and plant biodiversity, respectively. Because the current niche width model neglects several scenarios related to taxon and environmental attributes, it still needs to be treated with caution in predicting biodiversity trends.

Substrate quality drives fungal necromass decay and decomposer community structure under contrasting vegetation types

Abstract Fungal mycelium is increasingly recognized as a central component of soil biogeochemical cycling, yet our current understanding of the ecological controls on fungal necromass decomposition is limited to single sites and vegetation types. By deploying common fungal necromass substrates in a temperate oak savanna and hardwood forest in the midwestern USA, we assessed the generality of the rate at which high‐ and low‐quality fungal necromass decomposes; further, we investigated how the decomposer ‘necrobiome’ varies both across and within sites under vegetation types dominated by either arbuscular or ectomycorrhizal plants. The effects of necromass quality on decay rate were robust to site and vegetation type differences, with high‐quality fungal necromass decomposing, on average, 2.5 times faster during the initial stages of decay. Across vegetation types, bacterial and fungal communities present on decaying necromass differed from bulk soil microbial communities and were influenced by necromass quality. Moulds, yeasts and copiotrophic bacteria consistently dominated the necrobiome of high‐quality fungal substrates. Synthesis. We show that regardless of differences in decay environments, high‐quality fungal substrates decompose faster and support different types of decomposer micro‐organisms when compared with low‐quality fungal tissues. These findings help to refine our theoretical understanding of the dominant factors affecting fast cycling components of soil organic matter and the microbial communities associated with rapid decay.

Interactions between plants and soil shaping the root microbiome under abiotic stress.

Plants growing in soil develop close associations with soil microorganisms, which inhabit the areas around, on, and inside their roots. These microbial communities and their associated genes — collectively termed the root microbiome — are diverse and have been shown to play an important role in conferring abiotic stress tolerance to their plant hosts. In light of growing concerns over the threat of water and nutrient stress facing terrestrial ecosystems, especially those used for agricultural production, increased emphasis has been placed on understanding how abiotic stress conditions influence the composition and functioning of the root microbiome and the ultimate consequences for plant health. However, the composition of the root microbiome under abiotic stress conditions will not only reflect shifts in the greater bulk soil microbial community from which plants recruit their root microbiome but also plant responses to abiotic stress, which include changes in root exudate profiles and morphology. Exploring the relative contributions of these direct and plant-mediated effects on the root microbiome has been the focus of many studies in recent years. Here, we review the impacts of abiotic stress affecting terrestrial ecosystems, specifically flooding, drought, and changes in nitrogen and phosphorus availability, on bulk soil microbial communities and plants that interact to ultimately shape the root microbiome. We conclude with a perspective outlining possible directions for future research needed to advance our understanding of the complex molecular and biochemical interactions between soil, plants, and microbes that ultimately determine the composition of the root microbiome under abiotic stress.

Biochar application and summer temperatures reduce N2O and enhance CH4 emissions in a Mediterranean agroecosystem: Role of biologically-induced anoxic microsites

Biochar applications have been proposed for mitigating some soil greenhouse gas (GHG) emissions. However, results can range from mitigation to no effects. To explain these differences, mechanisms have been proposed but their reliability depends on biochar type, soil and climatic conditions. Furthermore, it is found that the mitigation capacity is dependent on how the biochar is aging under field conditions.The effects on N2O, CH4 and CO2 emission rates of a gasification pine biochar (applied as 0, 5, and 30 t ha−1) were studied between 8 and 21 months of the application in an alkaline soil cropped to barley under Mediterranean climate. Together with GHG, soil chemical and biological properties were assessed, namely, changes in labile organic matter content and nutrient status, and pH, as well as microbial abundance, activity, and functional composition.During the 2 years of the application, significant changes were observed at the highest rate of biochar application such as higher contents of water, K+, Mg2+, SO42−, higher basal respiration, and with non-significant changes in microbial community, though with some temporal effects. Regarding GHG, N2O decreases coupled with CH4 increases in the summer sampling were measured, although only for the highest application rate scenario. Such effects were unrelated to pH, bioavailable nitrogen status, or bulk soil microbial community shifts. We hypothesized that the key is the porous structure of our wood biochar, which is able to provide more and diversified microbial microhabitats in comparison to bulk soil. At higher temperatures in summer, biologically-induced anoxic conditions in biochar pores acting as microsites may be promoted, where total denitrification to N2 occurs which leads to N2O uptake, while CH4 production is promoted.

Long-term effects of biochar amendment on rhizosphere and bulk soil microbial communities in a karst region, southwest China

Biochar (BC) addition is widely used in agriculture to condition soils. However, the effects of BC addition on soil microbial community diversity and composition in karstic regions are unclear, especially after long-term application. To address this knowledge-gap, a field experiment was established to examine changes in soil physicochemical properties and microbial communities following six years of BC amendment. BC was applied to calcareous soils in a karstic region of southwestern China at four levels (w/w): 0%, 1.0%, 5.0%, and 10%. Bacterial community composition was then investigated in both the rhizosphere and bulk soils by 16S rRNA gene sequencing on the Illumina MiSeq Platform. BC addition increased soil pH, total carbon (TC), total nitrogen (TN), and total hydrogen (TH) contents in the rhizosphere and bulk soils. In addition, BC amendment was associated with changes in soil bacterial community compositions and diversities, especially at higher BC application levels. The relative abundances of Gemmatimonadetes increased in rhizosphere soils with increasing BC amendment, while those of the Bacteroidetes, Firmicutes, and Cyanobacteria decreased. The relative abundances of Proteobacteria and Chloroflexi increased in bulk soils with increasing BC application levels, while those of the Bacteroidetes and Verrucomicrobia decreased. Canonical correspondence analysis indicated that bacterial community composition was related to soil characteristics including pH, TC, TN, and TH contents in both rhizosphere and bulk soils. Importantly, variations in these soil parameters were closely associated with BC application rates. These results indicate that long-term BC application significantly impacts soil bacterial community characteristics in karstic regions via modulation of soil physiochemical properties.

Diversity patterns of the rhizosphere and bulk soil microbial communities along an altitudinal gradient in an alpine ecosystem of the eastern Tibetan Plateau

The diversity patterns and drivers of soil microbial communities in altitudinal gradients have recently received much attention. The rhizosphere is a focus of soil microbial communities, but the patterns and drivers of these communities have rarely been studied in alpine ecosystems. We used high-throughput Illumina sequencing to examine the community variations of bacteria, archaea and fungi between the rhizosphere and bulk soil along an altitudinal gradient in an Abies fabri (Mast.) community on Mount Gongga of the eastern Tibetan Plateau. Microbial alpha diversity and community structure varied significantly with altitude but not between the rhizosphere and bulk soil. Soil temperature and the carbon:nitrogen ratio were the primary drivers of the structures of the bacterial, archaeal and fungal communities, and altitude (geographic distance) contributed a small part (<3%) of the community variation, indicating that various edaphic factors were the key regulators of microbial-community variation. This consistency of the microbial communities between the rhizosphere and bulk soil in this alpine ecosystem could be attributed to low temperature and high nutrient content. The bacterial, archaeal and fungal communities were governed by specific environmental factors (total phosphorus content for bacteria; organic-carbon content, dissolved organic-carbon content, NH4+-N content and nutrient stoichiometry for archaea and NO3−-N content for fungi). The distinct environmental responses of the microbial taxa suggested metabolic separation and resource preferences of the belowground communities, even within the small-scale spatial distances in this alpine ecosystem. Our study suggested that the ecosystem harbored many microbial taxa with diverse nutrient preferences and metabolic characteristics and could thus potentially tolerate the soil environmental variation under a scenario of climate change.

Rhizosphere microbial communities of canola and wheat at six paired field sites

Plant physical and chemical characteristics are known to alter rhizosphere microbial communities, but the effect of introducing canola (Brassica napus L.) into monoculture wheat (Triticum aestivum L.) rotations is not clear. Results from a field study in eastern Washington showed that winter canola (WC) influenced the bulk soil microbial community and differentiated it from the community associated with winter wheat (WW). Abundance of soil fungi, including mycorrhizae, was reduced with the introduction of WC. The objective of this research was to determine the differences and similarities in the rhizosphere microbial communities of WC and WW. Canola and wheat rhizosphere soil was collected from six dryland farms in Adams and Douglas Counties, WA. Each farm was a paired site with WC and WW grown in adjacent fields of the same soil type, landscape orientation, and crop history. Canola, or any non-cereal crop, had never been grown previously at the experimental sites. Rhizosphere microbial biomass and community composition, determined using phospholipid fatty acid analysis (PLFA), revealed differences associated with landscape position at the initial fall sampling when WC and WW were in the rosette and tiller development stages, respectively. However, data from spring samples, when WC and WW were in the early bolting and stem elongation growth stages, respectively, showed significant differences in microbial communities between WC and WW rhizosphere soils. Data suggest that initial (fall) microbial community composition were an artifact of previous histories of monocrop wheat production and varied with expected differences in landscape position. As the crops developed, microbial communities became more dissimilar and were differentiated by crop species. Our results show that WC can have significant effects on rhizosphere microbial biomass of specific microbial groups and community structure in wheat-based cropping systems, such as reductions in fungi and gram+ bacteria in some locations. Crop-related changes in the abundance of specific rhizosphere microbial groups may play a key role in the yield of subsequent crops, and overall soil health and nutrient turnover.

Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities.

The effects of fertilizer regime on bulk soil microbial communities have been well studied, but this is not the case for the rhizosphere microbiome. The aim of this work was to assess the impact of fertilization regime on wheat rhizosphere microbiome assembly and 16S rRNA gene-predicted functions with soil from the long term Broadbalk experiment at Rothamsted Research. Soil from four N fertilization regimes (organic N, zero N, medium inorganic N and high inorganic N) was sown with seeds of Triticum aestivum cv. Cadenza. 16S rRNA gene amplicon sequencing was performed with the Illumina platform on bulk soil and rhizosphere samples of 4-week-old and flowering plants (10 weeks). Phylogenetic and 16S rRNA gene-predicted functional analyses were performed. Fertilization regime affected the structure and composition of wheat rhizosphere bacterial communities. Acidobacteria and Planctomycetes were significantly depleted in treatments receiving inorganic N, whereas the addition of high levels of inorganic N enriched members of the phylum Bacteroidetes, especially after 10 weeks. Bacterial richness and diversity decreased with inorganic nitrogen inputs and was highest after organic treatment (FYM). In general, high levels of inorganic nitrogen fertilizers negatively affect bacterial richness and diversity, leading to a less stable bacterial community structure over time, whereas, more stable bacterial communities are provided by organic amendments. 16S rRNA gene-predicted functional structure was more affected by growth stage than by fertilizer treatment, although, some functions related to energy metabolism and metabolism of terpenoids and polyketides were enriched in samples not receiving any inorganic N, whereas inorganic N addition enriched predicted functions related to metabolism of other amino acids and carbohydrates. Understanding the impact of different fertilizers on the structure and dynamics of the rhizosphere microbiome is an important step toward developing strategies for production of crops in a sustainable way.

Impacts of anaerobic soil disinfestation and chemical fumigation on soil microbial communities in field tomato production system

Anaerobic soil disinfestation (ASD), a potential alternative to pre-plant chemical fumigation for controlling soilborne pathogens, has been demonstrated in several agricultural production systems. The effect of ASD on the soil microbial community is considered one of the major factors responsible for pathogen suppression. However, rather limited information is available regarding the response of the soil microbial community to ASD throughout the cropping season, particularly in sandy soils. A field experiment was conducted to optimize the ASD technique for tomato production in Florida, utilizing two rates of molasses and composted poultry litter (CPL), and a pre-emergent herbicide application. The pre-plant soil treatments included ASD with 6.9 m3 ha−1 of molasses and 11 Mg ha−1 of CPL (ASD0.5), ASD with 13.9 m3 ha−1 of molasses and 22 Mg ha−1 of CPL (ASD1.0), and chemical soil fumigation control (CSF). The herbicide treatments included with and without halosulfuron application. Soil microbial community composition was monitored using phospholipid fatty acid (PLFA) analysis during the fall 2015 tomato production season. Halosulfuron application did not result in changes in the soil microbial community during the season. CSF led to significantly lower levels of bulk soil total microbial biomass, Gram negative bacteria, Gram positive bacteria and actinomycetes, compared to the ASD treatments. However, the rhizosphere effect of plants under CSF alleviated the microbial suppression and stimulated the growth of Gram negative bacteria and protozoa to reach similar levels to that of rhizosphere soils under the ASD treatments. Compared to 0 day after transplanting (DAT), Gram positive bacteria in bulk soils under the three pre-plant soil treatments significantly decreased while the fungi:bacteria ratio in bulk soils under CSF significantly increased at 36 DAT, and then remained stable throughout the season. Despite the similar microbial composition in bulk and rhizosphere soils between the two ASD treatments, the dynamic changes of some biomarker groups in bulk soils during 0–99 DAT showed distinct patterns particularly for total microbial biomass, Gram negative bacteria, actinomycetes, and fungi. Compared to 0 DAT, bulk soil microbial community composition shifted after 36 DAT under all soil treatments and remained stable until the end of the season. The changes in soil microbial community composition over time were related to changes in soil nutrient availability.

Responses of bulk and rhizosphere soil microbial communities to thermoclimatic changes in a Mediterranean ecosystem

The effect of thermoclimatic changes on microbial communities in the rhizosphere of a wild thyme species, Thymus zygis L., and its surrounding bulk soil was studied along elevational gradients in the Sierra Nevada National Park (Spain). Multiplex amplicon sequencing of bacterial and fungal taxonomic markers revealed that the richness, diversity and structure of bacterial and fungal communities were affected by thermoclimatic changes, with environmental parameters (mean annual atmospheric temperature and precipitation) and edaphic properties (mainly pH and nutrients) as the major drivers. Although both bulk soil and rhizosphere communities were structured according to the thermoclimatic zones, the response of microorganisms to thermoclimatic changes was different depending on the rhizosphere effect. On the contrary, the microbial functional gene diversity was not affected by thermoclimatic changes suggesting functional redundancy in the microbial communities along the altitudinal gradients. However, the functional gene diversity was clearly different between bulk soil and the rhizosphere, with the latter harbouring a larger number of gene copies and more different functional genes than bulk soils. Finally, a set of microbial bioindicators are defined for the thermoclimatic zones as a starting point to develop improved biological tools and models to monitor and predict the effects of climate changes. To the best of our knowledge, this is the first study where the response of bulk soil and rhizosphere microbial communities to thermoclimatic changes has been studied in parallel.

Fungal community assemblage of different soil compartments in mangrove ecosystem

The fungal communities of different soil compartments in mangrove ecosystem are poorly studied. We sequenced the internal transcribed spacer (ITS) regions to characterize the fungal communities in Avicennia marina root-associated soils (rhizosphere and pneumatophore) and bulk soil compartments. The rhizosphere but not pneumatophore soil compartment had significantly lower fungal species richness than bulk soil. However, bulk soil fungal diversity (Shannon diversity index) was significantly higher than both pneumatophore and rhizosphere soil compartments. The different soil compartments significantly affected the fungal community composition. Pairwise sample analyses showed that bulk soil microbial community composition significantly different from rhizosphere and pneumatophore soil compartments. There was, however no significant difference observed between rhizosphere and pneumatophore soil fungal community composition and they shared relatively more OTUs between them. Further, there was a significant correlation observed between fungal community compositional changes and carbon or nitrogen availability of different soil compartments. These results suggest that few characteristics such as fungal richness and taxa abundance of rhizosphere and pneumatophore soil compartments were significantly different in mangrove ecosystem.