Bacterial Community Structure Diversity Research Articles

Effects of Phosphogypsum and Suaeda salsa on the Soil Moisture, Salt, and Bacterial Community Structure of Salinized Soil

The improvement of saline soil is an important issue that cannot be ignored in the farmland soil environment. The change in soil salinity will inevitably affect the soil bacterial community. This experiment was based on moderately saline soil in the Hetao Irrigation Area, conducted by applying phosphogypsum (LSG), interplanting Suaeda salsa with Lycium barbarum (JP) and applying phosphogypsum and interplanting S. salsa with L. barbarum (LSG+JP),and the local unimproved soil of a L. barbarum orchard was used as the control (CK), to explore the effects of different improvement methods on soil moisture, salinity, nutrients, and bacterial community structure diversity during the growth period of L. barbarum. The results showed that compared with that under CK, the LSG+JP treatment significantly decreased the soil EC value and pH value from the flowering stage to the deciduous stage (P<0.05), with an average decrease of 39.96% and 7.25%, respectively; the LSG+JP treatment significantly increased soil organic matter (OM) and available phosphorus (AP) content during the whole growth period (P<0.05), with an average annual increase of 81.85% and 203.50%, respectively. The total nitrogen (TN) content was significantly increased in the flowering and deciduous stages (P<0.05), with an annual average increase of 48.91%. The Shannon index of LSG+JP in the early stage of improvement was increased by 3.31% and 6.54% compared with that of CK, and the Chao1 index was increased by 24.95% and 43.26% compared with that of CK, respectively. The dominant bacteria in the soil were Proteobacteria, Bacteroidetes, Actinobacteria, and Acidobacteria, and the dominant genus was Sphingomonas. Compared with that in CK, the relative abundance of Proteobacteria in the improved treatment increased by 0.50%-16.27% from the flowering stage to the deciduous stage, and the relative abundance of Actinobacteria in the improved treatment increased by 1.91%-4.98% compared with that in CK in the flowering and full-fruit stages. Redundancy analysis (RDA) results showed that pH, water content (WT), and AP were important factors affecting bacterial community composition, and the correlation heatmap showed that Proteobacteria, Bacteroidetes, and EC values were significantly negatively correlated (P<0.001); Actinobacteria and Nitrospirillum were significantly negatively correlated with EC values (P<0.01). In conclusion, the application of phosphogypsum and interplanting S. salsa with L. barbarum (LSG+JP) could significantly reduce soil salinity, increase nutrients, and improve the diversity of soil bacterial community structure, which is beneficial to the long-term improvement of saline soil in the Hetao Irrigation Area and the maintenance of soil ecological health.

The layout measures of micro-sprinkler irrigation under plastic film regulate tomato soil bacterial community and root system.

The change in rhizosphere soil bacterial community and root system under new water-saving device is not clear. A completely randomized experimental design was used to explore the effects of different micropore group spacing (L1: 30 cm micropore group spacing, L2: 50 cm micropore group spacing) and capillary arrangement density (C1: one pipe for one row, C2: one pipe for two rows, C3: one pipe for three rows) on tomato rhizosphere soil bacteria community, roots and tomato yield under MSPF. The bacteria in tomato rhizosphere soil were sequenced by 16S rRNA gene amplicon metagenomic sequencing technology, the interaction of bacterial community, root system and yield in tomato rhizosphere soil was quantitatively described based on regression analysis. Results showed that L1 was not only beneficial to the development of tomato root morphology, but also promoted the ACE index of tomato soil bacterial community structure and the abundance of nitrogen and phosphorus metabolism functional genes. The yield and crop water use efficiency (WUE) of spring tomato and autumn tomato in L1 were about 14.15% and 11.27%, 12.64% and 10.35% higher than those in L2. With the decrease of capillary arrangement density, the diversity of bacterial community structure in tomato rhizosphere soil decreased, and the abundance of nitrogen and phosphorus metabolism functional genes of soil bacteria also decreased. The small abundance of soil bacterial functional genes limited the absorption of soil nutrients by tomato roots and roots morphological development. The yield and crop water use efficiency of spring and autumn tomato in C2 were significantly higher than those in C3 about 34.76% and 15.23%, 31.94% and 13.91%, respectively. The positive interaction between soil bacterial community and root morphological development of tomato was promoted by the capillary layout measures of MSPF. The L1C2 treatment had a stable bacterial community structure and good root morphological development, which positively promoted the increase of tomato yield. The interaction between soil microorganisms and roots of tomato was regulated by optimizing the layout measures of MSPF to provide data support for water-saving and yield-increasing of tomato in Northwest China.

Effects of Cotton Stalk Returning on Soil Enzyme Activity and Bacterial Community Structure Diversity in Cotton Field with Long-term Saline Water Irrigation

Long-term saline water irrigation will increase soil salinity, adversely affect soil physical and chemical properties, and change the diversity of soil bacteria. Straw returning can improve the soil microenvironment and subsequently affect soil enzyme activity and bacterial community structure diversity. This experiment used two types of irrigation water salinity:fresh water (FW, 0.35 dS·m-1) and saline water (SW, 8.04 dS·m-1). Under each irrigation water salinity, the amount of cotton straw applied was 0 and 6000 kg·hm-2 (represented by FWST and SWST, respectively). The results showed that:compared with those under fresh water irrigation, saline water irrigation significantly increased the soil salt, bulk density, total carbon, and available phosphorus but significantly decreased available potassium content. Under saline water irrigation, straw returning significantly increased the soil total carbon, total nitrogen, available potassium, and available phosphorus but reduced soil bulk density. Compared with those under fresh water irrigation, soil sucrase, alkaline phosphatase, and catalase activities under saline water irrigation decreased by 57.24%, 35.15%, and 3.91%, respectively, whereas urease activity increased by 26.73%. However, straw returning significantly increased sucrase, alkaline phosphatase, and catalase activities but decreased urease activity. Saline water irrigation decreased the relative abundance of Acidobacteriota, Actinobacteriota, Bacteroidota, Verrucomicrobiota, and Firmicutes and increased the abundance of Gemmatimonadota and Myxococcota. Under saline water irrigation, straw returning significantly increased the relative abundance of Actinobacteriota, Bacteroidetes, Firmicutes, Crenarchaeota, Sphingomonas, Dongia, and Steroidobacter. NMDS results also showed that saline water irrigation and straw returning changed the bacterial community structure. In conclusion, straw returning can improve soil nutrient content, reduce soil bulk density and salinity, and then change soil enzyme activity and bacterial community structure diversity. The change in soil bacterial community composition was mainly affected by soil salinity and bulk density. Therefore, straw returning can improve soil fertility and help maintain the health of soil ecosystem. This study revealed a relationship between soil enzyme activities and bacterial communities, which provides a theoretical basis and mechanism for applying cotton stalk to regulate the soil enzyme and micro-ecological environment.

Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere

Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.

Effect of In Situ Bioremediation of Soil Contaminated with DDT and DDE by Stenotrophomonas sp. Strain DXZ9 and Ryegrass on Soil Microorganism

In the present study, the changes in the microbial populations, enzyme activity and bacterial community structure in contaminated soils were investigated during the bioremediation of using Stenotrophomonas sp. strain DXZ9 and ryegrass. The results showed that the removal rates were 81% for DDT and 55% for DDE (69% for DDTs) with ryegrass-microbe. Microbial activity was remarkably improved, and the number of bacteria increased sharply from 7.32 × 106 to 2.56 × 108 cells/g in the 10 days due to successful colonization of the strains and effects of the ryegrass rhizosphere. There was significant difference in fungi number with ryegrass when comparing the 30th and 90th days with the 210th day: The actinomycete number in the soil with ryegrass was higher than without ryegrass, and it indicated that the number of microorganisms significantly increased under the action of ryegrass. The activities of polyphenol oxidase, dehydrogenase and catalase were significantly activated by the combination of ryegrass and microbe, and urease activity was less affected: It has influence on the diversity of bacterial community structure in the soil, but its influence gradually decreased by denaturing gradient gel electrophoresis with an extension in time. The activities represented promising tools for decontaminating and restoring the ecosystem in sustainable ways, and proposing new approaches and technological bottlenecks to promote DDT biodegradation is very significant.

Changes in soil quality, bacterial community and anti-pepper Phytophthora disease ability after combined application of straw and multifunctional composite bacterial strains

Long-term implementation of intensive management in China has resulted in soil degradation and severe soil diseases. As the typical soil disease, pepper Phytophthora disease seriously affects the growth and development of many types of crops. To comprehensively address the problem of soil degradation and pepper Phytophthora disease, we have used a kind of novel multifunctional composite bacterial strains (MCBS) with excellent cellulose degradation and anti-pepper Phytophthora disease functions. In this study, we combined straw and this MCBS for the straw return experiment. The object of this study was to compare the influences of natural control without straw (CK), combined application of straw and MCBS (T1), and straw return under natural conditions (T2) on soil physicochemical properties, soil enzyme activity, soil bacterial community diversity, and soil anti-pepper Phytophthora disease (inhibiting the growth and reproduction of Phytophthora capsici that cause root rot, wilt, yellow wilt, vertical wilt, sudden collapse, black root, and stem rot of crops or reducing the negative impact from pepper Phytophthora diseases on crop growth and development). This study showed that the soil bulk density and specific gravity decreased by 6.57%, 1.58%, and 3.65%, 1.86% in T1 and T2 compared to CK. Soil total porosity, capillary porosity, non-capillary porosity, aggregate (>0.25 mm) and water-holding capacity increased by 5.85%, 5.00%, 7.61%, 26.64%, 20.52% and 2.93%, 1.29%, 6.33%, 7.73%, 14.71% in T1 and T2 compared to CK. The soil enzyme (urease, cellulase, alkaline phosphatase, and catalase) activity and soil chemical property increased with the straw return. Compared with CK, T1 significantly increased soil bacterial diversity, while T2 decreased soil bacterial community diversity. Bacterial of Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflex were the dominant phylum. T1 increased the relative abundance of nutrient and beneficial bacteria and decreased the relative abundance of oligotrophic and pathogenic bacteria. In addition, under the normal growth and Phytophthora capsici infected environment, plant height, stem thick, fresh weight and dry weight increased by 22.93%, 11.81%, 61.88% and 23.22% 49.72%, 23.29%, 118.70%, 65.22% in T1 compared to CK. In conclusion, combined application of straw and MCBS not only could significantly improve soil physicochemical properties, stimulate soil enzyme activity but alter soil bacterial community structure diversity and enhance soil pepper Phytophthora disease resistance ability. It helped to promote the sustainable development of Chinese agriculture.

Effects of Short-term Application of Moutai-flavor Vinasse Biochar on Nitrogen Availability and Bacterial Community Structure Diversity in Yellow Soil of Guizhou Province

To realize the comprehensive utilization of resources of moutai-flavor vinasse and improve the nitrogen efficiency of yellow soil, a field culture experiment was carried out to study the effects of short-term application of vinasse biochar on nitrogen availability and bacterial community structure diversity in yellow soil of Guizhou by setting 5 biochar dosages of 0% (MB0), 0.5% (MB0.5), 1.0% (MB1.0), 2.0% (MB2.0), and 4.0% (MB4.0). The results showed that the total nitrogen(TN) and nitrate nitrogen(NN) content in the soil increased by 35.79%-365.26% and 122.96%-171.80%, the microbial biomass nitrogen (MBN) content decreased by 34.10%-59.95%, and the AN/TN, NN/TN, and MBN/TN exhibited a decreasing trend with an increase in the amount of biochar applied. The application of vinasse biochar significantly reduced the number of OTU and community richness and diversity of soil bacteria; the influence degree increased with an increase in the application amount of vinasse biochar. In comparison with the MB0 treatment, the application of biochar significantly changed the soil bacterial community structure. The relative abundance of Bacteroidetes increased by 1.76-2.11 times with an increase in the biochar application. However, the relative abundance of Acidobacteria, Chloroflexi, Gemmatimonadetes, Planctomycetes, Armatimonadetes, Thaumarchaeota, and Nitrospirae decreased to different degrees, with the most significant decrease in the MB4.0 treatment. The application of vinasse biochar increased the relative abundance of certain soil functional bacteria, such as Streptomyces and Pusillimonas, and simultaneously also decreased the relative abundance of the dominant bacteria, such as Lysobacter and Gemmatimonas. In addition, the redundancy analysis (RDA) showed that the MBN/TN, NN, and MBN were the main cause of soil bacterial community structure change in nitrogen environment factor. The MBN/TN and MBN exhibited a significantly positive correlation with Thaumarchaeota and Nitrospira, which indicated that the short-term application of vinasse biochar can significantly reduce the abundance of ammonia-oxidizing archaea and nitrifying bacteria, inhibit the ammonia-oxidizing effect and nitrification rate of soil, and improve the availability of soil nitrogen. In summary, the short-term application of vinasse biochar can improve nitrogen nutrients, change the structure and diversity of soil bacterial community, and effectively control the risk of soil nitrogen leaching by inhibiting ammonia oxidation and nitrification of soil, to improve the availability of soil nitrogen.

The Effects of Organic and Mineral Fertilization on Soil Enzyme Activities and Bacterial Community in the Below- and Above-Ground Parts of Wheat

Bacterial community and soil enzymatic activity depend on soil and management conditions. Fertilization is an important approach to maintain and enhance enzyme activities and microbial community diversity. Although the effects of fertilizer application on soil microbial community and related parameters are explored, the effects on the soil microbiome associated with those of wheat plant organs, including those associated with roots and spikelets, are not well-known. Therefore, in this study, by using a sequencing approach, we assessed the effects of inorganic fertilizers, manure, and biochar on soil enzyme activities, bacterial community diversity and structure in the bulk soil, rhizosphere, roots, and spikelet of wheat (Triticumaestivum L.). For this, different treatment biochar (BC), manure (OM), low mineral fertilizer (HL), high mineral fertilizer (HF), and no fertilizer (FO) were used for the enzyme activities and bacterial community structure diversity tested. The result showed that organic amendment application increased total nitrogen, soil available phosphorus, and potassium compared to inorganic fertilizer and control, especially in the rhizosphere. Enzyme activities were generally higher in the rhizosphere than in the bulk soil and organic amendments increased activities of acid phosphatase (AcP), β-1,4-N-acetyl-glucosaminidase (NAG), and phenol oxydase (PhOx). Compared with soil and rhizosphere, bacterial diversity was lower in wheat roots and evenlower in the spikelet. From the bulk soil, rhizosphere to roots, the fertilization regimes maintained bacterial diversity, while organic amendment increased bacterial diversity in the spikelet. Fertilization regimes significantly influenced the relative abundances of 74 genera across 12 phyla in the four compartments. Interestingly, the relative abundance of Proteobacteria (Citrobacter, Pantoea, Pseudomonas, and unclassified Enterobacteriaceae) in the spikelet was decreased by increasing inorganic fertilizer and further by manure and biochar, whereas those of Actinobacteria (Microbacterium and an unclassified Microbacteriaceae) and Bacteroidetes (Hymenobacter and Chitinophagaceae) were increased. The results suggest that potential bacterial functions of both roots and above-ground parts of wheat would be changed by different organic amendment regimes (manure and biochar).

Clean and efficient utilization of coal combined with corn straw by synergistic biodegradation

To establish a process for cleaning and efficiently utilizing solid residues and residual liquid after co-fermentation of coal and corn straw, three coal samples combined with corn straw were used. Combustion tests were carried out using the solid residue to compare the changes in calorific value, slagging characteristics and air pollutant emission before and after fermentation. Biogas production experiments were performed using acclimated residual liquid to establish the biomethane production characteristics. Results show that the total calorific value of solid residue after co-fermentation of bituminous coal D, bituminous coal C and corn straw increased by 8.16% and 8.08%, respectively, compared to original samples. The slagging index also decreased during the combustion of solid residues. The diversity of bacterial community structure was the main causes for the significant reduction in air pollutant emissions from the combustion of solid residues. Acclimation experiments improved the removal rate of hemicelluloses from corn straw and increased biomethane production by 45.86%, 10.66% and 60.47%, respectively. This work can improve the clean conversion efficiency of coal and straw, not only reducing environmental pollution, but also transforming waste into clean energy, which has a positive impact on the environment and allows the sustainable use of resources.

Analysis of bacteria distribution characteristics in different layers of agarwood based on Hiseq sequencing

To explore the diversity of bacterial community structure between different layers of agarwood, Hiseq(high-throughput sequencing) was used to analyze the bacterial community structure of samples from different layers of agarwood. Our results showed that 1 150 096 optimized sequences and 9 690 OTUs were obtained from 15 samples of 5 layers of agarwood, which belonged to 28 bacterial phyla, 61 classes, 110 orders, 212 families and 384 genera. Further analysis revealed that the normal layer(NL) had the lowest bacterial species richness and the smallest number of OTUs. And the total number of OTUs of the agarwood layer(AL) and NL was zero, which was quite different.At the same time, there were significant differences in bacterial community structure and species diversity between NL and the other four layers. While there were some common dominant bacterial genera in both transition layer(TL) and NL. The similarity of bacterial distribution in 4 non-NL layers was relatively high, which had four common genera, such as Acidibacter, Bradyrhizobium, Acidothemus and Sphingomonas. While Acidibacter, Bradyrhizobium and Acidothemus were the dominant bacterial genus of DA and AL, and all of these layers contained volatile oil. In addition, the Bradyrhizobium was the most abundant in agarwood layer. Our results showed that bacterial community diversity and abundance were decreasing from DL to AL, and different layers showed significant differences in bacterial enrichment. It provided the clues to investigate how bacteria participate in the formation of agarwood.

Microbial community structure and distribution in the air of a powdered infant formula factory based on cultivation and high-throughput sequence methods

The air in a powdered infant formula (PIF) factory is a potential transfer medium for microorganisms. In this study, air samples from 6 main processing areas, almost covering the whole PIF processing line and 1 outdoor location, were collected from a PIF manufacturing plant during the winter and summer periods. A cultivation-based and an Illumina (San Diego, CA) high-throughput 16S rRNA sequencing method was used to investigate the community structures and distributions of bacteria in the air. High microbial diversity (25 genera, 56 species), with a dominant community including Staphylococcus, Bacillus, Acinetobacter, and Kocuria, was found by the cultivation-based method. Moreover, 104 genera were obtained from all samples by high-throughput sequencing methods. Lactococcus (32.3%), Bacillus (29.6%), and Staphylococcus (14.0%) were the preponderant genera. The indices from high-throughput sequencing results indicated that the bacterial community of the air samples was highly diverse. Significant differences in the diversity and distribution at 6 sampling locations were revealed using the 2 methods. In particular, the packaging process contained the highest proportion (39.4%) of isolated strains. The highest diversity in bacterial community structure was found in the outdoor location. More bacterial isolates and higher community diversity were observed in the summer samples compared with the winter samples. In addition, some pathogens, such as Acinetobacter baumannii, Bacillus cereus, and Staphylococcus cohnii, were mainly found in the large bag filling process, can filling, and packaging process areas. The present study provides greater insight into the microbial community and identifies potential sources of air contamination in PIF production environments and can serve as a guide to reduce the risk of microbial contamination in the production of PIF.

Effects of Endosulfan on the Populations of Cultivable Microorganisms and the Diversity of Bacterial Community Structure in Brunisolic Soil

Endosulfan, an organochlorine pesticide, has been applied ubiquitously worldwide. However, endosulfan has been identified as a type of persistent organic pollutants (POPs), and its ecotoxicity has drawn attentions from scientists. The present study was implemented to examine the effects of endosulfan on the diversity and structure of soil microorganism communities. A control treatment and three concentrations (0.1, 1.0, and 10.0 mg/kg) were set up in laboratory experiments and sampled on days 7, 14, 21, and 28. The results revealed that the populations of bacteria and actinomycetes decreased significantly after 1.0 and 10.0 mg/kg treatments and that the soil microbial biomass carbon (MBC) was increased by endosulfan compared with the control. Terminal restriction fragment length polymorphism (T-RFLP) results revealed that the soil bacterial diversity was decreased by endosulfan and that the soil microbial community structure became unstable after endosulfan application. Moreover, the results of a 16S rRNA clone library revealed that the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Spirochaetes, and Firmicutes showed an obvious advantage and closely relative. In conclusion, the results of the present study indicated that 0.1–10.0 mg/kg endosulfan showed obvious influences on the diversity and structure of the soil microbial community.