Response Of Soil Bacterial Communities Research Articles

Consistent responses of soil bacterial communities to bioavailable silicon deficiency in croplands

Soil bacterial communities play a crucial role in the maintenance of agro-ecosystem functions. Silicon (Si) fertilization has important impacts on the structure and function of soil bacterial communities. However, bioavailable Si in agricultural soils is projected to become depleted because of continuous intensive farming practices. It is urgently needed to investigate how bacterial communities respond to the Si deficiency in agricultural soils. Here, we reveal that the contents of the dissolved and reactive fractions of Si in soils have seriously decreased at the field scale. The reactive Si levels in the topsoil in rice fields (77.83 ± 41.14 mg/kg) were lower than the reported critical limit of Si for plant growth (85 mg/kg) and therefore require special attention. We investigated the composition of soil bacterial communities in these Si-deficient soils. Most dominant bacterial phyla and their subtaxa were significantly correlated with the reactive Si content. Modules II, IV, VI, and VIII within a co-occurrence network were significantly correlated with the reactive Si content. Notably, bacterial groups related to nitrogen, carbon, sulfur, and iron cyclings significantly changed in the Si-deficient soils. Soil reactive Si showed strong direct and indirect relationships with the composition of soil bacterial communities in croplands. The findings of this study will be useful for raising awareness of the need to improve agricultural Si fertilization for agro-ecosystem health and sustainability.

Different Responses of Soil Bacterial Communities to Nitrogen Addition in Moss Crust.

Bacterial communities in soil serve an important role in controlling terrestrial biogeochemical cycles and ecosystem processes. Increased nitrogen (N) deposition in Northwest China is generating quantifiable changes in many elements of the desert environment, but the impacts of N deposition, as well as seasonal variations, on soil bacterial community composition and structure are poorly understood. We used high-throughput sequencing of bacterial 16S rRNA genes from Gurbantünggüt Desert moss crust soils to study the impacts of N addition on soil bacterial communities in March, May, and November. In November, we discovered that the OTU richness and diversity of soil bacterial community dropped linearly with increasing N input. In November and March, the diversity of the soil bacterial community decreased significantly in the medium-N and high-N treatments. In May, N addition caused a substantial change in the makeup of the soil bacterial composition, while the impacts were far less apparent in November and March. Furthermore, the relative abundance of major bacterial phyla reacted non-linearly to N addition, with high-N additions decreasing the relative richness of Proteobacteria, Bacteroidetes, and Acidobacteria while increasing the relative abundance of Actinobacteria and Chloroflexi. We also discovered that seasonality, as characterized by changes in soil moisture, pH, SOC, and AK content, had a significant impact on soil bacterial communities. Significant variations in the makeup of the community were discovered at the phylum and genus levels throughout the various months. In May, the variety of soil bacterial community was at its peak. Further investigation showed that the decrease in soil bacterial diversity was mostly attributed to a drop in soil pH. These results indicated that the impact of N deposition on the soil bacterial community was seasonally dependent, suggesting that future research should evaluate more than one sample season at the same time.

Soil Bacterial Community Responses to N Application and Warming in a Qinghai-Tibetan Plateau Alpine Steppe

Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.

Vegetation restoration types affect soil bacterial community composition and diversity in degraded lands in subtropical of China

Significant improvement of soil quality and biodiversity has been reported following vegetation restoration on the degraded lands in subtropical of China. However, so far the response of soil bacterial communities and drivers of their composition to differing vegetation restoration types are not well understood. In this study, we investigated soil physicochemical properties and bacterial communities in degraded land subjected to differing vegetation restoration types after 12 years of long‐term experiment. Restoration types included grassland, cropland, three differing plantation forests (orchard, coniferous forest, and coniferous forest with applied tillage), and control of degraded land. Bacterial community composition was examined using 16S rDNA sequencing. Result found that soil nutrient content includes soil organic carbon (SOC), total N (TN), available nitrogen (AN), available phosphorus (AP), and available potassium (AK) was improved after 12‐year restoration and the highest contents were found in cropland. However, soil pH was decreased after revegetation in the order degraded land > grassland > forestland > cropland, and the soil C/N ratio was significantly decreased in cropland. Revegetation restoration significantly increased operational taxonomic units (OTUs), ACE, and Chao1 indices by 13.67–22.81%, 16.34–25.11%, and 14.66–24.00%, with relative abundances of bacterial phyla varying between the different vegetation types. Soil physicochemical properties (e.g. pH, SOC, TN, AN, AP, and AK) showed significant correlations with the majority of the dominant phyla. When degraded land was restored to cropland, soil C/N ratio decreased which promoted the growth of Actinobacteria. Revegetation with grassland and forest increased soil nutrient content and decreased pH, resulting in shifts in bacterial phyla favoring Proteobacteria and Acidobacteria. Our observations show that restoration of degraded land will lead to differing bacterial community compositions depending on the vegetation type.

Historical forest disturbance mediates soil microbial community responses to drought.

Despite the abundance of studies demonstrating the effects of drought on soil microbial communities, the role of land use legacies in mediating these drought effects is unclear. To assess historical land use influences on microbial drought responses, we conducted a drought-rewetting experiment in soils from two adjacent and currently forested watersheds with distinct land use histories: an undisturbed 'reference' site and a 'disturbed' site that was clear-cut and converted to agriculture ~60 years prior. We incubated intact soil cores at either constant moisture or under a drought-rewet treatment and characterized bacterial and fungal communities using amplicon sequencing throughout the experiment. Bacterial alpha diversity decreased following drought-rewetting while fungal diversity increased. Bacterial beta diversity also changed markedly following drought-rewetting, especially in historically disturbed soils, while fungal beta diversity exhibited little response. Additionally, bacterial beta diversity in disturbed soils recovered less from drought-rewetting compared with reference soils. Disturbed soil communities also exhibited notable reductions in nitrifying taxa, increases in putative r-selected bacteria, and reductions in network connectivity following drought-rewetting. Overall, our study reveals historical land use to be important in mediating responses of soil bacterial communities to drought, which will influence the ecosystem-scale trajectories of these environments under ongoing and future climate change.

Response of soil bacterial community to agricultural reclamation in the Tengger desert, northwestern China

Given the conditions of scarce soil water availability, high UV exposure and huge temperature fluctuation, plant growth in desert is extremely limited. In the last three decades, reclaiming desertified land for agricultural use via the application of solar greenhouse has been developing in the arid regions, northwestern China. However, the soil microbiome shift driven by the transformation of land use remains largely unexplored. To this end, we examined the diversity and composition of the bacterial community in the vineyard soil at the edge of Tengger desert, using the high-throughput quantitative 16S rRNA gene sequencing. Two types of agricultural managed soils, including those near the plant (PLT) and the others on the fertilization furrow (FTL), were collected. Soils from the open desert land without agricultural practices were used as the control (CON). The results showed that agricultural reclamation significantly (p < 0.05) reduced the desert soil bacterial diversity while promoted the total bacterial abundance from 106 copies up to 108 per ng of DNA, which increased up to 90 folds. Among the dominant bacteria Firmicutes, Proteobacteria, Actinobacteria, and Acidobacteria, Bacilli and Actinobacteria were found to be the keystone taxa responding to the agricultural practices especially to the nutrient inputs from fertilization. The functional prediction of the microbiome suggested that amino acid and carbohydrate transport and metabolism were the most important metabolic pathways differed between the three types of soils. Overall, our findings provide deep insights into the understanding of desert soil microbial responses to agricultural reclamation on the processes of human urbanization and reversion of desertification.

Changes in the root-associated bacteria of sorghum are driven by the combined effects of salt and sorghum development

BackgroundSorghum is an important food staple in the developing world, with the capacity to grow under severe conditions such as salinity, drought, and a limited nutrient supply. As a serious environmental stress, soil salinization can change the composition of rhizosphere soil bacterial communities and induce a series of harm to crops. And the change of rhizospheric microbes play an important role in the response of plants to salt stress. However, the effect of salt stress on the root bacteria of sorghum and interactions between bacteria and sorghum remains poorly understood.ResultsThe purpose of this study was to assess the effect of salt stress on sorghum growth performance and rhizosphere bacterial community structure. Statistical analysis confirmed that low high concentration stress depressed sorghum growth. Further taxonomic analysis revealed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Bacteroidetes and Firmicutes in sorghum rhizosphere soil. Low salt stress suppressed the development of bacterial diversity less than high salt stress in both bulk soil and planted sorghum soil. Different sorghum development stages in soils with different salt concentrations enriched distinctly different members of the root bacteria. No obviously different effect on bacterial diversity were tested by PERMANOVA analysis between different varieties, but interactions between salt and growth and between salt and variety were detected. The roots of sorghum exuded phenolic compounds that differed among the different varieties and had a significant relationship with rhizospheric bacterial diversity. These results demonstrated that salt and sorghum planting play important roles in restructuring the bacteria in rhizospheric soil. Salinity and sorghum variety interacted to affect bacterial diversity.ConclusionsIn this paper, we found that salt variability and planting are key factors in shifting bacterial diversity and community. In comparison to bulk soils, soils under planting sorghum with different salt stress levels had a characteristic bacterial environment. Salinity and sorghum variety interacted to affect bacterial diversity. Different sorghum variety with different salt tolerance levels had different responses to salt stress by regulating root exudation. Soil bacterial community responses to salinity and exotic plants could potentially impact the microenvironment to help plants overcome external stressors and promote sorghum growth. While this study observed bacterial responses to combined effects of salt and sorghum development, future studies are needed to understand the interaction among bacteria communities, salinity, and sorghum growth.

Insight to bacteria community response of organic management in apple orchard-bagasse fertilizer combined with biochar

Based on the sustainable development practice-zero growth in chemical fertilizer application, this article used bagasse organic fertilizer and rice husk derived biochar to investigate the response of soil bacterial community in apple orchard. Aimed at realize the soil quality improvement and biomass resource recovery to contribute agricultural and environmental sustainability. The co-trophic Proteobacteria was predominant in all the treatments (29–36 %) and enriched in non-nitrifying Alphaproteobacteria (9–11 %) and ammonia oxidant Betaproteobacteria (8–10 %), especially richest in bagasse fertilizer combine biochar treated soil. In addition, bacterial community variation was assessed by alpha and beta diversity, four treatments dispersed distribution and richer abundance observed in combined apply bagasse fertilizer and biochar treatment (3909.22 observed-species) than single application (3729.88 and 3646.58 observed-species). Biochar as microbial carrier combined organic fertilizer were established synergistic interaction and favorable to organic matter availability during sustainable agriculture. Finally, integrated biochar-bagasse fertilizer was richer than single organic or biochar fertilization in improving soil bacterial diversity, notably by promoting the metabolism of copiotrophic bacteria, nutrient cycling, plant growth and disease inhibit-related bacteria.

Soil bacterial community responses to short-term grazing exclusion in a degraded alpine shrubland – grassland ecotone

Grazing exclusion by fencing is a common and effective grassland management strategy for degraded grassland restoration. Soil bacteria, the most important decomposers of soil organic matter, is the linkage between plant and soil. However, soil bacterial α-diversity and community composition in the recover process of degraded shrubland – grassland ecotone on the Qinghai-Tibet Plateau has not been well understood. Thus, in this research, lightly and heavily degraded shrubland – grassland ecotone and its adjacent communities (alpine shrubland and alpine meadow) during recover process on the Qinghai-Tibet Plateau were selected to study α-diversity and community composition of soil bacteria, as well as the relationships among soil bacterial community, plant community and soil properties. Our results demonstrated that: 1) Dominant taxa at the phylum and genera level in all samples were similar. Proteobacteria, Acidobacteria and Bacteroidetes were dominant phyla, RB41, H16 and Ferruginibacter were dominant genera. 2) Grazing exclusion had no effect on soil bacterial α-diversity. However, grazing exclusion significantly decreased relative abundance of the Chloroflexi phylum, but grazing exclusion significantly increased the Elusimicrobia phylum relative abundance in the alpine meadow plot. 3) There were no significant differences on soil bacterial α-diversity between the heavily and lightly degraded grassland. However, relative abundance of the Planctomycetes phylum, Deltaproteobacteria class and RB41 genus in the alpine meadow plot of heavily degraded grassland were significantly lower than those in the lightly degraded grassland. 4) The higher plant community α-diversity and soil nutrition of shrubland – grassland ecotone did not result in a higher soil bacterial α-diversity. However, relative abundances of Chloroflexi phylum, Deltaproteobacteria class and Nitrospira class in the shrubland – grassland ecotone were significantly higher than those in the alpine meadow and alpine shrubland plots inside fence of the lightly degraded grassland. 5) Structural equation model (SEM) showed that soil organic carbon and soil total nitrogen were dominant factors affecting soil bacterial α-diversity. 6) Redundancy analysis (RDA) indicated that soil nitrate nitrogen and soil total nitrogen were the main driving factors for soil bacterial community composition. Our research found that the changes of soil bacterial α-diversity is incongruous with plant community α-diversity, while soil bacterial community composition is paralleled with plant community α-diversity and soil characteristics, especially the soil chemical property. These findings can provide management support for the restoration of degraded alpine shrubland.

Response of soil enzyme activity and bacterial community to copper hydroxide nanofertilizer and its ionic analogue under single versus repeated applications

Nanosized agrochemicals like nanofertilizers are being applied to soils. Adverse impacts of nanofertilizers on soil microflora were reported in past studies, but only considering a single application. Repeated applications are however more likely to occur in agriculture. We investigated effects of single versus repeated applications of a copper hydroxide nanofertilizer formulation (NFF) on soil enzyme activity and bacterial community. One or three applications were performed within 21 days to achieve same final level of Cu in soil (48 mg(Cu)/kg: the recommended dose of NFF). Besides, the active ingredient (i.e., copper hydroxide nanotubes (NT)) and dispersing agent (DA) of NFF, and an ionic fertilizer (i.e., CuSO4) were examined. Fluorescein diacetate hydrolase (FDAse), N-acetylglucosaminidase (NAG), leucine aminopeptidase (LAP), and urease (URE) showed negligible changes in the activities between the control and DA treatment. Bacterial community abundance, composition and diversity exhibited similar phenomena. Exposures to copper hydroxide NFF and NT or CuSO4 enhanced the activities of FDAse and NAG, weakened the activity of URE, and showed negligible changes in the LAP activity irrespective of single and repeated applications. Concentrations of NO3−-N and NH4+-N in soil were also affected by the application mode of NFF. More importantly, responses of soil bacterial community to copper hydroxide NFF were highly dependent on its application mode, whereas similar responses were observed in the CuSO4 treatment regardless of single or repeated applications. This study provided new insights into environmental risk of copper hydroxide NFF that were ignored in previous studies using a single exposure.

Response of soil bacterial communities to organic carbon input under soil freeze-thaw in forest ecosystems

The soil microbial community controls the biogeochemical cycle of elements critical to plant growth. Different carbon input modes have different effects on soil carbon storage and the microbial community, but the effects of carbon input control on soil microbial diversity and community structure in temperate forests remain unclear. We used high-throughput 16SrRNA gene sequencing and ecological network analysis methods to analyze the soil bacterial community, symbiotic network, and key species of three different carbon input treatments (litter removal, root removal, litter and root removal) in temperate natural secondary forests during the freeze-thaw season and growing season. The results showed that the change in the carbon source input led to a change in the way in which soil bacteria used carbon, which was mainly manifested as follows: (1) The relative abundance of Acidobacteria, which was oligotrophic bacteria, significantly decreased in the sample plots where the root system was removed. (2) In the litter removal treatment, the abundance of bacteria with functions related to the absorption of CH4 decreased. (3) The correlation between the module characteristic genes in the bacterial network analysis and the physical and chemical properties of soil, CK modules were grouped separately, and the change in the correlation may also indicate the change in the way soil bacteria use carbon. Second, the influence of belowground roots on the soil bacterial community structure was more significant than that of aboveground litter. The root system had a greater influence on the soil bacterial community. Third, the decrease of organic carbon input reduced the stability of the soil bacterial network, and the proportion of positive connections in the bacterial network for litter removal and root treatment increased significantly, indicating that these bacterial communities had the same change trend as the fluctuation of the environment. Finally, the freeze-thaw season had a greater impact than the growing season on bacterial diversity, community structure, and function. The freeze-thaw process allowed the bacterial community to respond to root removal more significantly, and the structural changes were mainly due to changes in temperature, water content, dissolved organic carbon, and nitrate nitrogen.

Common and management-specific responses of grassland soil bacterial communities to manure and chlortetracycline amendments

Manure application to soil affects the composition of soil bacterial communities as well as levels of antibiotic resistance genes in a manner dependent on various environmental and agricultural factors. These effects have been widely studied in arable soils, while the situation in grasslands that also receive inputs of fresh animal manure is largely unknown. Here, we focused on grassland soils under three different management types (pristine meadow, pasture, wintering pasture) from the same locality and compared the response of their bacterial communities to fresh cattle manure spiked or not with chlortetracycline. Soil microcosms were established either with soils (controls), + manure, + manure and chlortetracycline (CTC, 0.2 mg kg−1), and sampled at the same day (t0) and after 28 days (t28). Bacterial community composition was assessed by 454-pyrosequencing of 16S rRNA genes and correlations between the abundance of bacterial taxa and chosen tetracycline resistance genes (measured in our previous study) were calculated. Control soil bacterial communities at t0 differed significantly, reflecting differences in soil management history. Despite these initial differences, the responses of soil bacterial communities to cattle manure amendment showed similar trends in all three soils. Fresh cattle manure amendments significantly modified bacterial community structure in all soils at t0, increasing the relative abundance of OTUs affiliated to Clostridia and Bacilli. At 28d, all manure-amended soils showed a partial resilience, though they remained significantly different from controls. The effect of additional CTC was comparatively lower and only significant at t0 in all three soils. Several members of Firmicutes showed strong positive correlation with the abundance of tetracycline resistance genes tet(O), tet(Q) and tet(W), indicating that these taxa are potentially involved in dissemination of tetracycline resistance in manure-treated soils. In addition, this study indicated certain soil-management specific taxa, such as Geothrix and uncultured Burkholderiaceae, which could explain the previously observed differences in persistence of tetracycline resistance genes among soils.

Straw Incorporation with Nitrogen Amendment Shapes Bacterial Community Structure in an Iron-Rich Paddy Soil by Altering Nitrogen Reserves.

Incorporation of crop straw into the soil along with inorganic fertilization is a widespread agricultural practice and is essential in nutrient-scarce soils, such as iron-rich (ferruginous) paddy soils. The responses of soil bacterial communities to straw incorporation under different nitrogen inputs in iron-rich soils remain unclear. Therefore, 6000 kg ha−1 dry wheat (Triticum aestivum L. cv. Zhengmai 12) straw was applied to a rice paddy with and without nitrogen amendment (0, 80, 300, and 450 kg ha−1 N as urea), to investigate its effects on soil fertility and bacterial community structure. Organic matter, total nitrogen, and water contents tended to decrease in straw-incorporated soils with different nitrogen inputs. Proteobacteria was the dominant bacterial phylum across all treatments (26.3–32.5% of total sequences), followed by Chloroflexi, Acidobacteria, and Nitrospirae. Up to 18.0% of all the taxa in the bacterial communities were associated with iron cycling. Straw incorporation with nitrogen amendment increased the relative abundance of iron oxidizers, Gallionellaceae, while decreasing the relative abundance of iron reducers, Geobacteraceae. Bacterial community composition shifted in different treatments, with total nitrogen, water, and Fe(III) contents being the key drivers. Straw incorporation supplemented by 300 kg ha−1 N increased bacterial richness and enhanced all the predicted bacterial functions, so that it is recommended as the optimal nitrogen dosage in practice.

Characterisation of Bt maize IE09S034 in decomposition and response of soil bacterial communities

Returning straw to the soil is an effective way to improve the soil quality. As genetically modified (GM) crops experience expanded growing scales, returning straw to the soil could also be necessary. However, the impact of GM crop straws on soil safety remains unclear. The environment (including soil types, humidity and temperature) can result in a significant difference in the diversity of soil bacterial communities. Here, we compared the impacts of the straw from Bt maize IE09S034 (IE) and near-isogenic non-Bt maize Zong31 (CK) on soil bacterial community and microbial metabolic activity in three different environments. Sampling was carried out following 6–10 months of decomposition (May, June, July, and August) in three localities in Chinese cities (Changchun, Jinan, and Beijing). Our results showed that Bt maize residues posed no direct impact on soil bacterial communities in contrast to the environment and decomposed time. The microbial functional diversity and metabolic activity showed no significant difference between IE and CK. The results could be a reference for further assessing the effect of Bt maize residues on the soil that promotes the commercialisation of Bt maize IE09S034.

Response of soil bacterial communities, antibiotic residuals, and crop yields to organic fertilizer substitution in North China under wheat–maize rotation

Manure application can benefit soil quality and sustainable food productivity, but overapplication can spread high levels of antibiotics and antibiotic resistance genes. A two-year field experiment was conducted to evaluate the comprehensive impacts of organic fertilizer substitution in North China under a wheat–maize rotation. Four treatments were conducted: control (ZF), mineral fertilizer (MF), 50% nitrogen (N) mineral fertilizer substituted with organic fertilizer (MOF), and organic fertilizer (OF). Sulfonamide content, abundance of sulfonamide resistance (sul) genes, soil bacterial community, crop yield, and grain mineral elements were analyzed. Results showed that the MOF and OF treatments increased grain nutrients (phosphorus, potassium), and enriched sulfonamide residue and sul genes in soil. Additionally, the relative abundances of sul1 and sul2 in MOF and OF soils planted with maize were higher than in those planted with wheat. Compared to MF, the OF treatment decreased soil pH and crop yields but increased soil total nitrogen, phosphorus contents, and the abundance of Firmicutes. However, the MOF treatment significantly increased soil bacterial diversity and maintained yields of both wheat and maize. Increases in potential sul genes source bacteria (Planifilum), antibiotics, and soil nutrients accelerated the spread of sul genes in soil. Partial least squares path modeling analysis indicated that the soil bacterial diversity had a strong positive effect on maize yield. These results indicate that substitution of 50% N mineral fertilizer with organic fertilizer has the potential to benefit the stability and sustainability of the soil ecosystem, helping to meet the food demand in North China. However, the risk of antibiotics should be reduced through technical advances.

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.

Responses of soil bacterial community and enzyme activity to organic matter components under long-term fertilization on the Loess Plateau of China

Soil bacterial community structure, enzyme activities and their relationships to soil carbon and nitrogen in response to long-term fertilization remain poorly understood. Therefore, the objective of this study was to evaluate soil carbon and nitrogen fractions, enzyme activity, and bacterial community structure at 0–15, 15–30, and 30–60 cm depths after 34-yr of continuous application of manure and inorganic fertilizers. The study had a randomized complete block design with six treatments and three replications. Treatments were inorganic nitrogen fertilizer only (N), nitrogen plus phosphrous fertilizers (NP), manure (M), nitrogen plus manure (NM), nitrogen plus phosphorus plus manure (NPM), and unfertilized control (CK) in a winter wheat (Triticum aestivum L.) monoculture system. Most soil carbon and nitrogen fractions at 0–15 and 15–30 cm were greater with M, NM, and NPM, and winter wheat yield was greater with NPM than other treatments. The NPM increased β-glucosidase, β-xylosidase, and β-N-acetylglucosidase compared to other treatments at all depths. Soil bacterial Shannon index was similar among treatments at 0–15 and 15–30 cm and lower in N and NP than other treatments at 30–60 cm. Compared to CK, inorganic and manure fertilization increased relative abundances of Gemmatimonadetes and Bacteroidetes but decreased those of Nitrospirae, Planctomycetes, and Latescibacteria. Increases in soil enzyme activities and bacterial communities after long-term application of inorganic N and P fertilizers and manure was related to increased substrate availability. Overall, a combination of chemical fertilizers and manure can enhance soil health and quality through increased soil organic matter component, enzyme activity, and bacterial abundance.

Structural and Functional Shift in Soil Bacterial Community in Response to Long-Term Compost Amendment in Paddy Field

Microbial community composition and diversity of agricultural soils primarily depend on management practices. The application of compost on agricultural fields is known to increase soil fertility, which can also help to enhance agricultural productivity. The effects of long-term application of compost along with nitrogen (N), phosphorus (P), and potassium (K) (+Compost) on soil bacterial diversity and community profiles were assessed by amplicon sequencing targeting the 16S rRNA gene of bacteria and compared with those on soils that received only NPK but not compost (−Compost). Ordination plot showed treatments to cluster differently, implying changes in community composition, which were validated with taxonomical data showing Firmicutes, Actinobacteria, and their related classes to be significantly higher in +Compost than in −Compost soils. The predicted abundance of functional genes related to plant growth promotion, development, and decomposition was significantly higher in compost-amended soil than in soils without compost. The results are of particular importance as they provide insights into designing management practices to promote agricultural sustainability.

Response of soil bacterial communities to nitrogen and phosphorus additions in an age-sequence of subtropical forests

With global nitrogen (N) deposition continuously increasing, few reports exist describing how soil bacteria respond at the molecular level to long-term addition of excess N in variously aged forests. To reveal the responses of soil bacteria to the elevated N, an experiment was conducted with a chronic nutrient addition within differently aged stands (46-, 78-, and 200-years-old) in the northern subtropical China since 2011, including three treatments, CK (no N nor phosphorus (P) additions), N treatment (N, 100 kg N ha-1), and N with P (N+P, 100 kg N ha-1 + 50 kg P ha-1) to examine potential P limitation under N deposition. Metagenomic sequencing was used to examine the snapshot responses of soil bacterial communities. Soil moisture and texture, ammonium, nitrate, SOC (soil organic carbon), TN (soil total nitrogen), TP (total phosphorus), DOC (dissolved organic carbon), DON (dissolved organic nitrogen) were measured to explain the influence mechanism of forest age and fertilization on changes of microbial community. Following N addition, soil bacterial community diversity and most dominant phyla increased, but they showed a decrease with increasing stand age. The effects of fertilization on the same taxa were variable across forest ages. Soil bacterial community responded differently in 7-year fertilization, with distinct shift in 46-year-old forest and adaptability to long-term N addition in the 200-year-old forest. Soil texture and moisture, DOC, DON, pH, SOC/TN and TP were significantly correlated with bacterial community across stand ages, while N fertilization affected the bacterial community mostly via inducing soil moisture, NO3--N, DOC and pH in the 46-year-old forest, whose effects decreased with increasing stand age. Our results suggest that due to the variation of soil physicochemical properties among forest ages, soil bacterial communities are more stable and resilient to N deposition with increasing the age of stands. Soil bacterial communities might not encounter P limitation following the long-term addition of N in the subtropics.

Biodegradation of di-n-octyl phthalate by Gordonia sp. Lff and its application in soil

ABSTRACT A previous isolated Gordonia sp. (Lff) was used to degrade di-n-octyl phthalate (DOP) contamination in both aqueous solution and soil. The influence of temperature, pH, inoculum size, salt content and initial concentration of DOP on DOP degradation by Lff were analysed. The response of soil bacterial community to DOP and Lff was also analysed by Illumina MiSeq sequence method. Results showed that the optimal temperature, pH, inoculum size and salt content were 35oC, 8.0, 5% and <5%, respectively. Under the optimal condition, more than 91.25% of DOP with different initial concentrations (100–2000 mg/L) could be degraded by Lff. Kinetics analysis indicated that biodegradation of DOP by Lff could be described by first-order kinetics (R 2 > 0.917) with the half-life (t 1/2) changing irregularly between 0.58 and 0.83 d. In addition, Lff enhanced the removal of DOP in soil and alleviated the toxicity of DOP on soil microorganisms. Furthermore, its influence on soil bacterial community is not obvious. These results suggested that Lff was effective in remediating DOP contamination in different environments.