Community Structure Of Soil Bacteria Research Articles

Altitude Distribution Characteristics of Farmland Soil Bacteria in Loess Hilly Region of Ningxia

It is of great significance for the conservation of biodiversity in farmland ecosystems to study the diversity, structure, functions, and biogeographical distribution of soil microbes in farmland and their influencing factors. High-throughput sequencing technology was used to analyze the distribution characteristics of soil bacterial diversity, community structure, and metabolic function along elevation and their responses to soil physicochemical properties in farmland in the loess hilly areas of Ningxia. The results showed that:① The Alpha diversity index of soil bacterial was significantly negatively correlated with elevation (P < 0.05) and showed a trend of decreasing and then slightly increasing along the elevation. ② Seven phyla, including Proteobacteria, Actinobacteria, and Acidobacteria, were the dominant groups, and five of them showed highly significant differences between altitudes (P < 0.01). ③ At the secondary classification level, there were 36 metabolic functions of bacteria, including membrane transport, carbohydrate metabolism, and amino acid metabolism, of which 22 showed significant differences, and 12 showed extremely significant differences among different altitudes. ④ Pearson correlation analysis showed that soil water content, bulk density, pH, and carbon-nitrogen ratio had the most significant effects on bacterial Alpha diversity, whereas soil nutrients such as total organic carbon, total nitrogen, and total phosphorus had significant effects on bacterial Beta diversity. ⑤ Mantel test analysis showed that the soil water content, total organic carbon, and carbon-nitrogen ratio affected bacterial community structure at the phylum level, and soil pH, total organic carbon, total nitrogen, total phosphorus, and carbon-nitrogen ratio were significantly correlated with bacterial metabolic function. Variance partitioning analysis showed that soil water content had the highest explanation for the community structure of soil bacteria, whereas soil pH had the highest explanation for metabolic function. In conclusion, soil water content and pH were the main factors affecting the diversity, community composition, and metabolic function of soil bacteria in farmland in the loess hilly region of Ningxia.

Response of soil microorganisms to soil fertility in the process of vegetation rehabilitation of degraded Pinus massoniana forest

AbstractThe rehabilitation of diverse and three‐dimensional forest vegetation patterns is crucial for preventing forest degradation and improving soil fertility. However, the relationship between soil microbial community and soil fertility was not clear. To accurately assess the capability of vegetation restoration measures on the real impact on degraded soil ecosystems. We selected three vegetation rehabilitation models of degraded Pinus massoniana forests in typical soil erosion areas in China as the research objects, with untreated bare land as the control. All three vegetation construction patterns increased the abundance and diversity of soil bacteria and fungi, thereby enhancing the stability of the soil ecosystem. Additionally, the vegetation rehabilitation models also altered the community structure of soil bacteria and fungi in the degraded P. massoniana forests. The pH and soil fertility index (IFI) were the main factors leading to variations in the community structure of the soil bacteria and fungi. Among them, the grass‐planting model showed a significantly greater improvement in the soil fertility of degraded P. massoniana forests than the shrub‐planting and arbor‐planting models. Furthermore, Ascomycota, Basidiomycota, and Glomeromycota exhibited the most significant response to IFI, indicating their potential as indicator microorganisms for soil fertility changes. The improvement in soil fertility in degraded P. massoniana forests was influenced primarily by the increase in urease activity (S‐UE) according to the vegetation rehabilitation models (84.20%, p = 0.000). In conclusion, the grass‐planting system effectively improved the soil ecosystem quality of degraded P. massoniana forests in southern erosion‐prone areas of China and was suitable for further application.

Modifying soil bacterial communities in saline mudflats with organic acids and substrates.

The high salinity of soil, nutrient scarcity, and poor aggregate structure limit the exploitation and utilization of coastal mudflat resources and the sustainable development of saline soil agriculture. In this paper, the effects of applying exogenous organic acids combined with biological substrate on the composition and diversity of soil bacterial community were studied in moderately saline mudflats in Jiangsu Province. A combination of three exogenous organic acids (humic acid, fulvic acid, and citric acid) and four biological substrates (cottonseed hull, cow manure, grass charcoal, and pine needle) was set up set up on a coastal saline mudflat planted with a salt-tolerant forage grass, sweet sorghum. A total of 120 kg ha-1 of organic acids and 5,000 kg ha-1 of substrates were used, plus two treatments, CK without application of organic acids and substrates and CK0 in bare ground, for a total of 14 treatments. No significant difference was found in the alpha diversity of soil bacterial community among all treatments (p ≥ 0.05), with the fulvic acid composite pine needle (FPN) treatment showing the largest increase in each index. The beta diversity differed significantly (p < 0.05) among all treatments, and the difference between citric acid-grass charcoal (CGC) and CK treatments was greater than that of other treatments. All treatments were effective in increasing the number of bacterial ASVs and affecting the structural composition of the community. Citric acid-cow manure (CCM), FPN, and CGC treatments were found to be beneficial for increasing the relative abundance of Proteobacteria, Chloroflexi, and Actinobacteria, respectively. By contrast, all treatments triggered a decrease in the relative abundance of Acidobacteria. Among the 12 different combinations of exogenous organic acid composite biomass substrates applied to the coastal beach, the CGC treatment was more conducive to increasing the relative abundance of the salt-tolerant bacteria Proteobacteria, Chloroflexi and Actinobacteria, and improving the community structure of soil bacteria. The FPN treatment was more conducive to increase the species diversity of the soil bacterial community and adjust the species composition of the bacterial community.

Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and grape quality in vineyards

Abstract Pesticides can have unintentional effects on non‐target organisms and change biotic communities. Such changes might be particularly important in soil microbial communities, which drive many ecosystem functions and may affect crop quality. Here, we investigated, in a three‐year study, how vegetation control (by herbicide application) and soil copper content (from long‐term copper‐based fungicide application) affect biodiversity and the community structure of soil bacteria, fungi and protists, and associated soil functions (respiration, decomposition) in Swiss vineyards. Furthermore, we determined the effects of these two management practices on grape quality as the most direct ecosystem service to farmers. Across all study years, the community composition of microorganisms was affected by herbicide application, however, a significant loss of operational taxonomic units (OTUs) was only observed in fungi and protists. Soil copper content reduced OTU richness of bacteria and protists in some years but had no significant effect on fungal richness. Copper changed the community composition in all three groups of soil microorganisms. While we found no effect of copper on soil functions, herbicide application reduced microbial respiration and biomass by about 39% and 45%, respectively. However, decomposition rates remained virtually unchanged by any pesticide. Yeast assimilable nitrogen (YAN) levels in grape were below the critical threshold of 140 mg/L in 40% of the vineyards without herbicide application and the variety Chasselas, whereas in vineyards with herbicide application, it was only 20%. Application of pesticides led to changes in richness and composition of soil microbial communities and directly reduced some soil functions (microbial biomass and respiration) but not all (decomposition). Some grape quality parameters can be indirectly enhanced by pesticide application, highlighting the trade‐off between the interests of nature conservation and the interests of the farmer. Balancing these two diverging interests requires the establishment of alternative vineyard management allowing reduced pesticide application.

Epigallocatechin gallate (EGCG) nanoselenium application improves tea quality (Camellia sinensis L.) and soil quality index without losing microbial diversity: A pot experiment under field condition

Applying selenium (Se) fertilizer is the only way to alleviate soil Se deficiency. Although effects of nanoselenium foliar application on plant growth and stress resistance have been extensively investigated, soil application of nanoselenium on soil microorganisms and their relationship with crop quality and soil health remains unclear. In this study, a steady-state homogeneous nanoparticle of epigallocatechin gallate Se (ESe) was synthesized, and a pot experiment was conducted applying ESe at five concentrations (0, 1, 10, 50, and 100 mg kg−1) to the tea planattion soil. The study revealed a significant increase in Se concentration in soil and tea with ESe application and identified 2.43–7.8 mg kg−1 as the safe and optimal range for soil application. Specifically, the moderate dose of ESe improved the tea quality [reduced tea polyphenols (TP), increased free amino acids (AA), and reduced TP/AA] and soil quality index (SQI). Besides, in marure tea leaves, antioxidant enzyme activities [promote catalase (CAT) superoxide dismutase (SOD), and peroxidase (POD)] increased, while level of oxidative stress [malondialdehyde (MDA), hydrogen peroxide (H2O2) and superoxide anion (O2−)] decreased with ESe application. The 16S rRNA of the soil bacteria showed that ESe application significantly changed the community structure of soil bacteria but did not alter the diversity of the bacteria and the abundance of dominant taxa (phylum and genus levels). Statistical analysis of the taxonomic and functional profiles (STAMP) detected 21 differential taxa (genus level), mainly low-abundance ones, under the ESe application. Linear regression and random forest (RF) modeling revealed that the low-abundance bacterial taxa were significantly correlated with SQI (R2 = 0.28, p < 0.01) and tea quality (R2 = 0.23–0.37, p < 0.01). Thus, the study's findings suggest that ESe application affects soil and tea quality by modulating the low-abundance taxa in soil. The study also highlights the crucial role of low-abundance bacterial taxa of the rhizosphere in regulating soil functions under the ESe application.

Biochar alleviates the crop failure of rice production induced by low-nitrogen cultivation mode by regulating the soil microbes taxa composition.

To improve the nitrogen utilization efficiency and a series of environmental problems caused by excessive application of nitrogen fertilizer, actual agricultural production often reduced the usage ratio of nitrogen fertilizer. However, the reduction in nitrogen fertilizer not only affects the soil microenvironment but also leads to adverse effects on rice yield. Due to its unique properties, biochar can regulate soil nutrient distribution and significantly affect soil microbial community structure/functions. To further understand the effects of different levels of biochar on soil nutrient indicators, soil microorganisms and crop growth under the nitrogen-reduction condition, our experiment with four groups was set up as followed: 0%, 2.5% and 5% biochar application rates with 99kg/hm2 nitrogen fertilizer and one control group (the actual fertilizer standard used in the field:110kg/hm2) without no exogenous biochar supplement. The rice yield and soil nutrient indexes were observed, and the differences between groups were analyzed based on multiple comparisons. 16S ribosomal RNA and ITS sequencing were used to analyze the community structure of soil bacteria and fungi. Redundancy analysis was performed to obtain the correlation relationships between microbial community marker species, soil nutrient indexes, and rice yield. Path analysis was used to determine the mechanism by which soil nutrient indexes affect rice yield. The results showed that a higher application rate of biochar led to a significant increased trend in the soil pH, organic matter and total nitrogen content. In addition, a high concentration of biochar under nitrogen-reduction condition decreased the soil bacterial diversity but elevated the fungal diversity. Different concentrations of biochar resulted in these changes in the relative abundance of soil bacteria/fungi but did not alter the dominant species taxa. Taken together, appropriate usage for biochar under the nitrogen-reduction background could induce alteration in soil nutrient indicators, microbial communities and crop yields. These results provide a theoretical basis for exploring scientific, green and efficient fertilization strategies in the rice cultivation industry. Notably, the interaction relationship between rhizosphere microorganisms in rice and soil microbial taxa are not yet clear, so further research on its detailed effects on rice production is needed. In addition, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis for the physiological functions of the soil microbes could only predict the potential metabolic pathways. Therefore, the next-generation metagenome techonology might be performed to explore detailed metabolic differences and accurate taxa alteration at the "species" level.

Effect of Brassinolide on Soil Microorganisms in Millet Field Polluted by Tribenuron-Methyl.

Tribenuron-methyl is used to control broad-leaved weeds and has a promising application prospect in millet fields. However, its negative impact on soil ecology cannot be ignored. Brassinosteroids have been widely reported to enhance plant resistance to stress, but information on brassinosteroids for the remediation of pesticide-contaminated soils is limited. Under field conditions, brassinosteroids were applied to explore their effects on the residues of tribenuron-methyl, soil enzyme activity, soil microbiol community, and millet yield. After applying brassinosteroids according to the dose of 150 mL hm-2, the degradation rate of tribenuron-methyl accelerated. Brassinolide stimulated the activities of catalase and dehydrogenase, while the activities of sucrase and alkaline phosphatase were inhibited. The results of high-throughput sequencing showed that brassinosteroids inhibited the growth of Verrucomicrobia, Ascomycota, and Mortierellomycota and promoted the abundance of cyanobacteria. Additionally, brassinosteroids could also significantly increase the diversity index and change the community structure of soil bacteria and fungi. Further, the predicted function results indicated that brassinosteroids changed some metabolic-related ecological functions of the soil. We also found that brassinolide could increase millet yields by 2.4% and 13.6%. This study provides a theoretical basis for the safe use of tribenuron-methyl in millet fields and a new idea for the treatment of pesticide residues in soil.

Effects of nitrogen reduction combined with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard.

Understanding soil bacterial diversity under nitrogen reduction is necessary for the crucial role in soil nitrogen cycling. However, the effects of combined fertilization on soil chemical properties, microbial community structure, and yield are unknown. This study was conducted to investigate the effect of nitrogen fertilizer reduction with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard. Six treatments were set in this study: NF-100%, NF-75%, NF-50%, NF-25% and CF, no nitrogen fertilizer and bio-organic fertilizer for CK. The bacterial community structures of soil were analyzed by 16S rRNA gene amplification high-throughput sequencing technology. Nitrogen fertilizer reduction with bio-organic fertilizer increased soil organic matter (SOM), total nitrogen (TN), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), available potassium (AK), and reduced soil pH. NF-50% and NF-25% treatments increased the yield of red raspberry. Nitrogen reduction combined with bio-organic fertilizer increased the relative abundance of copiotrophic bacteria and decreased the relative abundance of oligotrophic bacteria. The increase in copiotrophic bacteria in the soil of red raspberry orchard could indicate an increase in soil nutrient availability, which have positive implications for soil fertility and production. However, nitrogen fertilizer reduction with bio-organic fertilizer altered the abundance and diversity of soil bacteria, which was reduced compared to CF treatments. The PCoA analysis of the soil bacterial community showed that the community structure of NF-25% treatment was more different from other treatments, indicating that the fertilization method changed the community structure of soil bacteria. The results of a redundancy analysis showed that SOM, pH, AN, TN, and AP were the main factors affecting the microbial community structure. Overall, the reduction of nitrogen fertilizer with bio-organic fertilizer significantly increased the soil nutrient content, reduced the relative abundance and diversity of soil bacteria, increased the relative abundance of beneficial bacteria in the soil, changed the bacterial community structure of soil, increased production and created suitable soil conditions for the red raspberry growth.

Impacts of shelterbelt systems on pasture production and soil bacterial and fungal communities in agricultural fields

AbstractIntroductionShelterbelts, which provide protection for livestock and crops against severe weather conditions, have been recognised as important contributors to increased crop yields. Soil microorganisms play important roles in nutrient cycling, soil health and plant performance, thereby exerting significant influence on ecological services in terrestrial ecosystems. However, impacts of shelterbelts on soil microbial communities in pasture ecosystems remain poorly studied.Materials and MethodsHere, we assessed the effect of shelterbelts (composed of Eucalyptus and native shrubs) on the pasture and nutrient productivity as well as soil bacterial and fungal communities at four distances from the shelterbelts with two different heights in two fields during spring and summer by applying amplicon sequencing, physicochemical and nutritional value analyses.ResultsThe results showed that the shelterbelt height, distances from shelterbelts, seasons and their interactive effects substantially affected pasture yield, neutral detergent fibre, metabolisable energy and crude protein yields, but did not increase the pasture productivity in the rows adjacent to the shelterbelts. We also identified that the alpha diversity of bacteria and fungi did not significantly change across distances from the shelterbelts in both fields, but the community structure of soil bacteria and fungi was significantly influenced by distances from the shelterbelts. Interestingly, soil calcium (Ca) and shelterbelts were identified as top predictors of fungal community while soil pH and Ca was key drivers of bacterial community.ConclusionOur study provides novel knowledge in the impact of shelterbelts on pasture and nutritional production and soil microbial communities, which contributes to appropriate application and strategic management of the windbreak systems in agriculture production.

Effects of wildfire disturbance on forest soil microbes and colonization of ericoid mycorrhizal fungi in northern China

Wildfires affect forest succession and restoration by changing the community structure of soil microorganisms. Mycorrhizal formation is essential for plant growth and development. However, the driving mechanism of their natural succession after wildfire is still unclear. In this study, we examined the community structure of soil bacteria and fungi along a time series of natural recovery after wildfires in the Greater Khingan Range of China (2020 fires, 2017 fires, 2012 fires, 2004 fires, 1991 fires, and unburned). By exploring the effects of wildfire on plant traits, fruit nutrition, colonization of mycorrhizal fungi and its influencing mechanism. The results show that natural succession after wildfires significantly changed the community composition of bacteria and fungi, with β diversity having a greater impact but less impact on the α diversity of microorganisms. Wildfires significantly changed plant traits and fruit nutrient content. The changes in colonization rate and customization intensity of mycorrhizal fungi were caused by increased MDA content and soluble sugar content and increased MADS-box gene and DREB1 gene expression in lingonberry (Vaccinium vitis-idaea L.). Our results showed that the soil bacterial and fungal communities in the boreal forest ecosystem changed significantly during wildfire recovery and changed the colonization rate of lingonberry mycorrhizal fungi. This study provides a theoretical basis for the restoration of forest ecosystems after wildfires.

Taxonomic and functional responses of soil and root bacterial communities associated with poplar exposed to a contamination gradient of phenanthrene.

Polycyclic aromatic hydrocarbon (PAH) contamination of industrial wasteland soils affects microbial diversity, but little is known about the dose-response effects of such contaminants on taxonomic and functional diversities of rhizospheric and plant endophytic bacteria. This study focused on the response of soil and root bacterial communities associated to poplar grown in a contamination gradient of phenanthrene (PHE). It was hypothesized that the increase in contamination would modify gradually the bacterial diversity and functions. The effects of the PHE contamination were limited to soil communities and did not affect the poplar root endophytome where Streptomyces and Cutibacterium were the most abundant genera. Along the PHE gradient, alpha-diversity indices decreased and the community structure of soil bacteria at the taxonomic level shifted. The abundance of genes involved in PAH-degradation pathways and the relative proportion of certain microbial taxa such as Polaromonas, Sphingopyxis, Peredibacter, Phenylobacterium, Ramlibacter, Sphingomonas, and Pseudomonas, often described as potential PAH biodegraders, increased with the PHE concentration in the soil community. Conversely, the contamination negatively impacted other taxa like Nocardioides, Streptomyces, Gaiella, Solirubrobacter, Bradyrhizobium, and Nitrospira. Functional inference and enzymatic activity measurements revealed that some bacterial functions related to carbon, nitrogen and phosphorus cycles were modified in soil throughout the PHE gradient. This study allowed a deeper understanding of the complex plant-bacteria interactions in the case of soil PAH contamination and the potential impact on soil functioning.

Response of Soil Microbial Communities to Elevation Gradient in Central Subtropical Pinus taiwanensis and Pinus massoniana Forests

In forest ecosystems, elevation gradient is one of the most influential factors on soil characteristics, vegetation types, and soil microorganisms. However, it remains unclear how the elevation gradient and the soil environment under its influence affect soil microbial communities under two distinct vegetation types. In this study, high-throughput sequencing technology from Illumina was utilized to examine the response of soil microbial communities to elevation and their driving factors in forests of Pinus taiwanensis and Pinus massoniana in various Jiangxi Province locales. The results demonstrated that the elevation gradients of the two pines had significant effects on soil organic carbon (SOC) and total nitrogen (TN), both in unimodal mode as well as on the alpha diversity of soil microbes. The community structure of soil bacteria is more sensitive to elevation than that of soil fungus. At different elevations in the two pine forests, Acidobacteria, Proteobacteria, Chloroflexi, Verrucomicrobia, Bacteroidetes, Patescibacteria, and Thaumarchaeota are the dominant bacterial phyla, and Ascomycota, Basidiomycota, and Mucoromycota are the dominant fungal phyla. This investigation revealed that SOC and TN were the two most influential factors on the alteration of the soil microbial community in two pine forests. In summary, there were substantial changes in soil microbial diversity and community composition across the two different pine forests, with elevation and soil characteristics (SOC and TN) serving as the primary drivers.

Biochar derived from hydrolysis of sewage sludge influences soil properties and heavy metals distributed in the soil.

Sewage sludge contains a large number of nutrients and dangerous substances, when sludge was processed into sludge hydrochar that was added to the soil, which not only solve the problem of sludge disposal, but also amend the soil and fix pollutants in the soil. However, it was lack of report on the effect of the sludge hydrochar on soil compositions and soil microorganism community structures until now. In the present study, the hydrothermal carbonization method is used to prepare hydrochar from sewage sludge at temperatures of 180℃ and 240℃ at durations of 6h and 15h in this paper. The effects of the prepared sludge hydrochar on soil-derived dissolved organic matter (DOM), the content of total dissolved nitrogen (TDN) and NO3--N in soil, and the community structure of soil bacteria and fungi were evaluated. Furthermore, the change rules in heavy metal speciation in soils treated with sludge hydrochar were investigated. With the increase in the preparation temperature and dosage of sludge hydrochar, the main components of DOM changed from soluble microbial byproducts to fulvic acid-like and humic acid-like fractions through UV and fluorescence characterization. The sludge hydrochar prepared at low temperature could significantly increase the contents of TDN and NO3--N in the soil. Affected by sludge hydrochar, the dominant phylum of the bacterial community changed from Proteobacteria to Actinobacteria, and the dominant phylum in the fungal community did not change, but its relative abundance increased. Finally, the sludge hydrochar obtained when the carbonization time was 15h was more beneficial to reduce the total amount and available content of heavy metals in the soil. The study provides a basis for sludge hydrochar application for the soil amendment.

Study on Diversity of Culturable Bacteria in Maize Field Soil under Pesticide Stress

The effects of pesticide application on the diversity of culturable bacteria in the soil of corn farmland in Sanjiang Plain were studied, and the bacteria capable of degrading acetochloramine in the soil samples were screened. In the black soil of corn farmland where “ethyldiazine 86” was applied, the experimental group and the control group were set, and the culturable bacteria in the soil samples of the two groups were cultured and screened by coating plate method. The 16S rRNA gene sequences and morphological characteristics were analyzed to determine the species of bacteria. Selective medium was designed to screen pesticide degrading bacteria. 19481 strains of culturable bacteria were cultured in the experiment, including 7854 strains in the experimental group and 11627 strains in the control group. A total of 65 strains were screened, purified and preserved, including 16 strains of phosphorus solubilizing bacteria, 9 strains of nitrogen fixing bacteria and 4 strains of pesticide degrading bacteria. The community structure of soil bacteria was mainly composed of Pseudomonas, Pantoea and Bacillus, and the dominant bacterium was Pseudomonas. The four pesticide-degrading bacteria were all Pseudomonas migulae. Long-term application of pesticides can reduce the number of culturable-bacteria in the soil, and the bacteria richness is also decreased. This study provides a theoretical basis for understanding the bacterial diversity of pesticide residue soil, protection and sustainable utilization of black soil.

Effects of Land Reclamation on Soil Bacterial Community and Potential Functions in Bauxite Mining Area.

Studying the characteristics of microorganisms in mine reclamation sites can provide a scientific reference basis for mine land reclamation. Soils in the plough layer (0-20 cm) of the bauxite mine plots in Pingguo city, Guangxi Zhuang Autonomous Region, China, with different reclamation years were used as the research objects. The community structure of soil bacteria was analyzed with high-throughput sequencing technology. The results show the following: (1) Reclamation significantly increased the contents of soil nutrients (p < 0.05). (2) The relative abundances of Proteobacteria were high (22.90~41.56%) in all plots, and reclamation significantly reduced the relative abundances of Firmicutes (3.42-10.77%) compared to that in the control plot (24.74%) (p < 0.05). The relative abundances of α-proteobacteria generally increased while the reclamation year increased. The relative abundances of α-proteobacteria and γ-proteobacteria showed significant positive correlations with soil carbon, nitrogen, and phosphorus nutrients (p < 0.01). The relative abundance of Acidobacteria Group 6 showed significant positive correlations with soil exchangeable Ca and Mg (p < 0.01). (3) Bacterial co-occurrence network showed more Copresence interactions in all plots (50.81-58.39%). The reclaimed plots had more nodes, higher modularity, and longer characteristic path length than the control plot, and the keystone taxa changed in different plots. (4) The chemoheterotrophy and aerobic chemoheterotrophy were the most abundant functional groups in all plots (35.66-48.26%), while reclamation reduced the relative abundance of fermentation groups (1.75-11.21%). The above findings indicated that reclamation improved soil nutrients, changed the bacterial community structure and potential functions, and accelerated the microbial stabilization of the reclaimed soil.

Effects of single and combined contamination of microplastics and cadmium on soil organic carbon and microbial community structural: A comparison with different types of soil

Microplastics (MPs) are an emerging contaminant that have attracted a growing concern about their behavior in soil environment in recent years. However, the research on the interaction between MPs and heavy metal pollution in the soil environment is still scarce. This study investigated the effects of high–density polyethylene (HDPE) and Cd on two soil types (phaeozem and fluvo–aquic soil), and explored their interaction mechanisms. The addition of HDPE significantly increased the content of available Cd in the phaeozem and enhanced the soil organic carbon (SOC) content and the abundance of microbial available carbon source. The presence of Cd reduced the content of SOC and dissolved organic carbon (DOC) in phaeozem and changed the soil bacteria community structure. The combined pollution of HDPE and Cd had a superimposed effect on the increment of DOC content in fluvo–aquic, and in phaeozem, the combined pollution had an antagonistic effect on SOC and DOC. In conclusion, the coexistence of MPs and Cd would affect soil carbon cycling and microbial community structure, especially in phaeozem. These results contribute to understanding the effects of MPs and/or Cd on soil biological properties.

Impact of Drip Irrigation and Nitrogen Fertilization on Soil Microbial Diversity of Spring Maize.

Given the shortage of water resources and excessive application of nitrogen fertilizers in irrigated areas, we explored the effect of water−nitrogen coupling on soil microbial diversity in maize fields irrigated using shallow buried droppers. A field experiment (split-plot design) was used with irrigation amounts set at 40%, 50%, and 60% of the conventional amount; furthermore, 13 water and nitrogen coupling treatments were designed. The secondary area was the nitrogen application level, corresponding to 50%, 70%, and the original conventional application amounts. The results showed that the effect of irrigation amount on bacterial community composition was greater than that of nitrogen, whereas the effect of nitrogen on fungi was greater than that on bacteria. No significant difference was detected in the α diversity index or species richness of bacteria and fungi. Available phosphorus and organic carbon contents significantly correlated with the community structure of soil bacteria (p < 0.05). The relative abundances of bacteria and fungi were stable with the decrease of nitrogen application rate at the irrigation rate of 2000 m3 ha−1. With the decrease of irrigation amount, the relative abundance of bacteria and fungi was stable under the treatment of 210 kg ha−1 nitrogen fertilizer. Moreover, the relative abundance of nitrogen-fixing bacteria related to the nitrogen cycle was increased by irrigation of 2000 m3 ha−1 and nitrogen application of 210 kg ha−1. Moderate reduction of subsequent N supply should be as a prior soil management option in a high N input agroecosystem.

Effects of David Deer Grazing on Soil Bacterial and Fungal Communities in an Eastern Coastal Wetland of China

The grazing activity of animals has a significant role on the environmental modification of land. In the coastal wetlands of eastern China, long-term David deer (Elaphurus davidianus) grazing has caused the degradation of various ecological elements in the area. Still, few studies have been reported concerning the effects of David deer grazing on the soil microorganisms of their habitats. We analyzed the community structure of soil bacteria and fungi in an area of continuous annual grazing and another area without traces of David deer grazing so as to learn about the effects of deer grazing on the soil microbial community structure in a spatial instead of temporal way, in preparation for improving the environment for deer survival. David deer grazing drastically changed the physicochemical characteristics of the soil, accelerating the alkalinization process and inhibiting the buildup of nutrients. There were differences in the microbial community structure between the grazed and the control areas, with bacteria predominating. The control had a higher level of bacterial and fungal alpha-diversity than the grazed area. The makeup of the soil’s microbial community was also influenced, except for the dominant microbial at the phylum level. In addition to the establishment of numerous complex fungal functional types, David deer grazing increased the number of bacterial functional types linked to the carbon cycle. The impacts of soil pH and urease activity on bacterial and fungi populations were highlighted using the redundancy analysis. This study demonstrates that David deer grazing changes and complicates microbial functional kinds of composition, as well as modifies the composition of the soil’s microbial community, improving the soil nutrient cycling process, mainly the carbon element.

Amplicon-based assessment of bacterial diversity and community structure in three tropical forest soils in Kenya

Forest soils provide a multitude of habitats for diverse communities of bacteria. In this study, we selected three tropical forests in Kenya to determine the diversity and community structure of soil bacteria inhabiting these regions. Kakamega and Irangi are rainforests, whereas Gazi Bay harbors mangrove forests. The three natural forests occupy different altitudinal zones and differ in their environmental characteristics. Soil samples were collected from a total of 12 sites and soil physicochemical parameters for each sampling site were analyzed. We used an amplicon-based Illumina high-throughput sequencing approach. Total community DNA was extracted from individual samples using the phenol-chloroform method. The 16S ribosomal RNA gene segment spanning the V4 region was amplified using the Illumina MiSeq platform. Diversity indices, rarefaction curves, hierarchical clustering, principal component analysis (PCA), and non-metric multidimensional scaling (NMDS) analyses were performed in R software. A total of 13,410 OTUs were observed at 97% sequence similarity. Bacterial communities were dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Acidobacteria in both rainforest and mangrove sampling sites. Alpha diversity indices and species richness were higher in Kakamega and Irangi rainforests compared to mangroves in Gazi Bay. The composition of bacterial communities within and between the three forests was also significantly differentiated (R = 0.559, p = 0.007). Clustering in both PCA and NMDS plots showed that each sampling site had a distinct bacterial community profile. The NMDS analysis also indicated that soil EC, sodium, sulfur, magnesium, boron, and manganese contributed significantly to the observed variation in the bacterial community structure. Overall, this study demonstrated the presence of diverse taxa and heterogeneous community structures of soil bacteria inhabiting three tropical forests of Kenya. Our results also indicated that variation in soil chemical parameters was the major driver of the observed bacterial diversity and community structure in these forests.

Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production.

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.