Richness Of Soil Bacterial Communities Research Articles

Effects of organic materials on soil bacterial community structure in long-term continuous cropping of tomato in greenhouse.

Long-term fertilization will affect the above-ground vegetation, but we have little understanding of soil bacterial community structure and diversity so far. This study aims to study the effect of organic fertilization on the soil bacterial community structure and diversity of protected long-term continuous tomato cropping by using high-throughput sequencing technology. Results show that (1) fertilization application (chemical fertilizer [CF] and vermicompost [VM]) significantly changed the soil physico-chemistry properties, such as soil pH decreased compared with control treatment and increased the soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), and total potassium (TK) contents; (2) VM increased the Shannon index of soil bacteria but decreased the soil Chao1 index; and (3) soil Proteobacteria and Actinomycetes were dominant taxa and the relative abundance of Actinobacteria increased by 36.40–44.27 and 25.80–29.35%, with CF and VM, respectively, compared with the control. Pearson correlation analysis showed that soil pH, SOC, TN, TP, and TK were the main environmental factors that affected the diversity and richness of soil bacterial communities. Redundancy analysis (RDA) showed that the SOC and TN play important roles in the composition of soil bacterial communities. In summary, the effect of VM on the soil bacterial community structure of continuous tomato cropping is better than that of CF, which should be used in the sustainable production of facility tomatoes.

Soil bacteria around a derelict tailings pile with different metal pollution gradients: community composition, metal tolerance and influencing factors.

Bacteria play a vital role in ecological processes of soil contaminated by heavy metals. Here, soil sampling was carried out around a tailings pile contaminated to different degrees by cadmium (Cd), lead (Pb) and arsenic (As). The bacteria in the soil were cultured, separated and purified on Luria-Bertani medium, and the changes in bacterial communities in soils with different pollution levels were analysed with 16S rRNA sequencing. Bacillus pacificus strain MZ520364 was found to be highly tolerant to Cd, Pb and As, and single-metal and multimetal tolerance experiments were further conducted with this strain. The results obtained from alpha diversity and operational taxonomic unit (OTU) statistical analyses showed a significant difference in bacterial composition among soils with different metal pollution levels, and the highest bacterial diversity was found at the most severely polluted site. Evidence from variance partitioning analysis (VPA) and the Spearman correlation heatmap analysis showed that the leading factors affecting bacterial community composition were cation exchange content (CEC), pH, total Zn, total As, and available As concentrations in soil. Additionally, in the single-metal treatments, B. pacificus MZ520364 could tolerate 600mg/L Cd2+, 1000mg/L Pb2+ or 700mg/L As3+. When Cd, Pb and As coexisted, the best growth of B. pacificus MZ520364 was present at 120mg/L Cd2+, 200mg/L Pb2+ and 150mg/L As3+. The effect of Cd, Pb and As on the growth of the strain followed the order of Cd > As > Pb, and the heavy metal combination showed more toxicity than single metals. In summary, our results revealed the ecological impact of soil physicochemical properties on the diversity and richness of soil bacterial communities and suggested that B. pacificus MZ520364 may be used for the remediation of Cd-Pb-As co-contaminated soil.

Partial substitution of chemical fertilizer with organic fertilizer over seven years increases yields and restores soil bacterial community diversity in wheat–rice rotation

Substituting chemical fertilizer with organic fertilizer is an important agricultural practice that improves crop yields but also affects soil biogeochemical cycling. To explore the effects of organic fertilizer on soil properties and bacterial community structure and diversity, a long-term field experiment (2011–2017) was conducted in a wheat–rice rotation system with four treatments: control (CK, no fertilizer), chemical fertilizer only (NPK), substitution of 50% of chemical nitrogen (N) fertilizer with organic fertilizer (NPKM), and substitution of 100% of chemical N fertilizer with organic fertilizer (OM). Results showed that, crop yields (wheat and rice) from 2011–2017 were highest in NPKM. Combined with α-diversity analysis, long-term application of NPK led to a decrease in soil bacterial diversity. However, soil bacterial community richness (Ace and Chao1 indices) increased in NPKM in the wheat season, as well as in OM in the rice season. Compared with NPK, organic fertilizer inputs (NPKM and OM) increased microbial biomass carbon and abundance of dominant bacteria (Acidobacteria, Anaerolineaceae, and Nitrospira) in both crop seasons. In NPK, relative abundance of Rhodanobacter increased significantly in the wheat season because of low soil pH. Bacterial community composition and structure were similar between NPKM and OM in the wheat season. Redundancy analysis further found that soil pH (R2 = 0.735, P = 0.013) co-varied with the bacterial community structure in the wheat season. In the rice season, relative abundance of Nitrospira increased significantly in NPKM, which could generate large amounts of nitrate nitrogen (NO3−-N), and then increase risks of N2O emissions and NO3−-N leaching in paddies. Overall, partial substitution of chemical fertilizer with organic fertilizer was optimal to increase crop yields and recover soil bacterial diversity in the wheat–rice rotation, and greater substitution with organic fertilizer in combination with chemical fertilizer is recommended only for rice seasons.

Vegetation richness, species identity and soil nutrients drive the shifts in soil bacterial communities during restoration process.

Soil bacteria play an essential role in functioning of ecosystems and maintaining of biogeochemical cycles. However, little is known about changes in the compositions and functional groups of soil bacterial communities during different restoration stages. The influences of aboveground vegetation and belowground soil properties on soil bacterial communities were also unclear during this process. Here we sequenced the soil bacterial communities in different stages of sand fixation. Sand fixation increased the diversity of the bacterial communities, among which the populations of Actinobacteria, Acidobacteria and Gemmatimonadetes changed significantly. The function prediction showed sand fixation increased Gram-positive and aerobic bacteria. Bacterial structure is significantly correlated with plant richness, coverage and biomass. In particular, we found species identity was an important determinant in structuring bacterial composition. Soil properties were all significantly correlated with soil bacterial community richness and diversity. Fusobacteria was strongly positively correlated with sand, Chloroflexi with total N and Gemmatimonadetes with SOM and total C. It suggested that soil nutrients (TC, TN and SOM) have large consequences for soil bacterial community dissimilarities. These results indicated that vegetation richness, especially species identity, together with improvement in soil nutrients, play key roles in driving the shifts in soil microbial community structure and function during restoration process.

Bacillus amyloliquefaciens Biofertilizer Mitigating Soil Ammonia Volatilization

In this study, we investigated the effectiveness and microbial mechanism of Bacillus amyloliquefaciens biofertilizer on reducing ammonia volatilization in farmland soil. Pot experiments were carried out to explore the effects of B. amyloliquefaciens biofertilizer (BB) and chemical fertilizer on soil ammonia volatilization, crop yield and quality, and soil microbial community. Four fertilization strategies were tested, namely no fertilizer (CK), 100% chemical fertilizer (C), 50% BB and 50% chemical fertilizer (B1), and 100% BB (B2). The dynamic flow-through chamber method was used to determine the soil ammonia volatilization flux after fertilization. The soil bacterial community during the peak period of ammonia volatilization was analyzed using 16S rDNA high-throughput sequencing. The results showed that the amount of ammonia volatilization in B1 and B2 decreased by 79.5% and 84.8%, respectively, as compared with treatment C. B2 had the lowest nitrate content and the highest yield; the yield of B2 increased by 50.5% and 12.3% as compared to that of CK and C, respectively. B1 had the highest content of vitamin C, which was 67.6 mg ·kg-1. The application of BB improved the diversity and richness of soil bacterial community, especially the relative abundance of Bacillus and Nitrospira. This shows that BB plays an important role in preventing air pollution and improving nitrogen utilization.

Response of soil characteristics and bacterial communities to nitrogen fertilization gradients in a coastal salt‐affected agroecosystem

AbstractUnderstanding the relationship between fertilization and soil bacterial communities in a salt‐affected environment is essential for alleviating the adverse impact of excessive salinity on soil biochemical functioning. However, how soil bacterial communities respond to consecutive fertilization across nitrogen gradients in coastal agroecosystem has not yet been clarified. We conducted a field plot experiment with four nitrogen fertilization rates (0, 150, 300, and 450 kg N hm−2 yr−1) on coastal salt‐affected soil for three consecutive years. Temporal dynamics of soil chemical and microbial properties was characterized, and soil bacterial community composition against N fertilization rates was investigated using 16S rRNA gene sequencing. Results indicated that consecutive N fertilization significantly increased soil organic carbon, total nitrogen (TN), available nitrogen (AN), available phosphorous, microbial biomass carbon (MBC), microbial biomass nitrogen and net nitrogen mineralization rate (NMR). N fertilization rates and cultivation years exhibited interactive effect on TN, AN, MBC and NMR. Soil bacterial community richness and diversity increased with the nitrogen rates. Predominant bacterial classes were Deltaproteobacteria, Anaerolineae, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria and Planctomycetia. Increasing nitrogen fertilization resulted in an elevation in the relative abundance of classes Alphaproteobacteria, Gammaproteobacteria, Planctomycetia and Nitrospira, and a decline in Anaerolineae, Acidobacteria_Gp6, Cytophagia, Bacilli and Acidobacteria_Gp10. Community composition of Alphaproteobacteria, Planctomycetia and Nitrospira was significantly associated with potential nitrification rate (PNR), whereas that of Actinobacteria was relevant to carbon mineralization rate. Results underlined that nitrogen fertilization improved nutrients, biochemical characteristics and metabolic activities to create more suitable bacterial microhabitats in the coastal agroecosystem.

Metagenomic analysis of diversity and composition of soil bacteria under intercropping system Hevea brasiliensis and Canna indica

Composition of soil microbiomes plays important ecological roles and vital ecosystem processes in nature of soil. Indeed, interaction between plant root, microbes, and soil influences significantly biologically, physically and chemically of soil properties. In this study, high throughput sequencing of 16S rRNA gene of soil bacteria using Illumina platform was performed for analyzing composition, richness and biodiversity of soil bacteria in two different soil conditions. Two soil samples from Rubber tree – Canna indica intercropping areas and two soil samples from area without C. indica were collected and analyzed the diversity and richness of soil bacterial communities. Bioinformatic data analysis showed in average more than 5500 bacterial OTU were identified in each soil samples. Relative abundance of individual OTU between soil with and without C. indica showed statistically no difference. From 30 phyla that have been identified in both soil conditions, only 5 phyla (BH180.139, Cyanobacteria, Proteobacteria, TM6, and WS3) showed a statistically different (p < 0.05) in their abundance. A total 270 and 355 Familia and Genus respectively were identified. There is no statistically difference in richness, abundance and diversity of species between both soil conditions. However, intercropping soil with C. indica showed lower species abundance in comparison with soil without C. indica (ACE index 112 and 125, 6 respectively). In contrast, soil with C. indica has more taxa richness in comparison with soil without C. indica (Fisher index 278 and 230, 4, respectively).

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Biogeography and the driving factors affecting forest soil bacteria in an arid area

Bacteria are one of the most abundant and diverse groups and mediate many critical terrestrial ecosystem processes. Despite the crucial ecological role of bacteria, our understanding of their large-scale biogeography patterns across longitude (east-west transect), and the processes that determine these patterns lags significantly behind that of macro-organisms. Here, we used 16S rRNA gene sequencing to evaluate the geographic distributions of bacterial diversity and their driving factors across different longitude sites along an 800-km east-west transect in the Loess Plateau. Twenty-four phyla were detected across all soil samples and the most sequence-abundant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Chloroflexi and Gemmatimonadetes (average relative abundance >5%). Soil bacterial α-diversity, expressed by the richness of soil bacterial communities and Shannon diversity, differed among climates (MAP) but showed strong correlations with MAP (r=−0.537 and r=−0.42, respectively; p<0.05 in both bacterial diversity indices). Variation partition analysis demonstrated that the bacterial community structure was closely correlated with environmental variables and geographic distance, which together explained 62% of the community variation. Soil properties contributed more to bacterial community variation than the combined geographic distance (historical contingencies) and climate factors. Among all environmental factors, soil pH exhibited a dominant role in structuring bacterial communities in this arid area. Our findings provide new evidence of bacterial biogeography patterns in an arid area (MAP ranged from 473mm to 547mm). Additionally, the results indicated a close linkage among soil bacterial community, climate and edaphic variables, which is critical for predicting promoting sustainable ecosystem services in the Loess Plateau.

Responses of Soil Bacterial Communities to Conyza canadensis Invasion with Different Cover Classes Along a Climatic Gradient

Some invasive species can trigger shifts in soil microbial communities in their rhizosphere to facilitate the invasion process. Meanwhile, some invasive species can display different cover classes in the invaded ecosystems and even cross many climatic zones. This study aims to address the effects of the notorious invasive species Conyza canadensis with different cover classes along a climatic gradient in China on soil bacterial communities. All cover classes of C. canadensis increased the Shannon's diversity index and the abundance‐based coverage estimator (ACE) index but decreased the operational taxonomic richness and the Good's coverage of soil bacterial communities, although this change was not significant. Thus, C. canadensis invasion can raise the diversity and richness of soil bacterial communities but also leads to the extinction of some soil microbial species to create a microenvironment that facilitates its further invasion. The increased diversity and richness of soil bacterial communities induced by C. canadensis invasion with different cover classes may play an important role in its successful invasion across multiple climatic zones. This may be due to the fact that soil microbial communities can influence plant communities and higher soil bacterial diversity can improve soil functions and plant nutrient acquisition. Meanwhile, the effect size and the significance level of climatic gradient on the ACE index and the Chao1 index of soil bacterial communities was obviously higher than other indices of soil bacterial communities. Thus, species richness of soil bacterial communities was primarily changed under C. canadensis invasion along a climatic gradient.

Application of Bio-organic Fertilizer to Control Tomato Fusarium Wilting by Manipulating Soil Microbial Communities and Development

A pot culture experiment was conducted in soils with a 3-, 5-, or 10-year history of continuous cropping. Results showed that with increasing years of continuous cropping, biomass, soil and plant analyzer development (SPAD) readings, root activity, superoxide dismutase (SOD) activity, and malondialdehyde (MDA) content gradually decreased. After bio-organic fertilizer (BOF) application, biomass, SPAD readings and root activity, SOD activity, and MDA content gradually increased compared to controls. Similarly, catalase (CAT) and guaiacol peroxidase (POD) activity decreased with increasing years of continuous cropping, and increased substantially in BOF-treated soil compared to the control soil. The diversity and richness of soil bacterial community declined, while those of fungal community increased as continuous cropping increased. BOF application led to substantial increases in quantities of soil rhizosphere bacteria and actinomycetes and significant decreases in quantities of soil fungi. The soil bacterial community showed the greatest changes, whereas the fungal community showed the fewest changes.

English

A new exotic weed, Flaveria bidentis, is spreading in central China where it forms dense monospecific patches modifying the structure of different native ecosystems and threatening native aboveground biodiversity. However, little is known about the consequences of such an invasion for soil bacterial community, especially its effect pattern at different invasion stages. In this study, soil samples were taken in native ecosystems that were uninvaded, partially invaded (transition), and severely invaded by F. bidentis. The bacterial richness and diversity in F. bidentis in rhizospheres soil was evaluated using denaturing gradient gel electrophoresis (DGGE) analysis. Different stages of F. bidentis invasion can trigger changes in soil physicochemical properties in particularly in available N and P F. bidentis invasion significantly decreased the richness of soil bacterial community, and the decline contents were positively correlated with invasion progress. In the invaded soils, bacterial species in Proteobacteria , Chloroflexi and Actinomycetes decreased with invasion, with the greatest reduction in relative abundance occurring for Proteobacteria, which was the dominant species in the native soils. Invasion of F. bidentis corresponded with an alteration in the structure of soil bacterial community, and soil microbial biomass as well, thus soil environment modification was expected to promote spreading of this exotic weeds in turn. Key words : Biological invasion, Flaveria bidentis, soil nutrients, soil bacteria, polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE).

Metagenomic and Small-Subunit rRNA Analyses Reveal the Genetic Diversity of Bacteria, Archaea, Fungi, and Viruses in Soil

Recent studies have highlighted the surprising richness of soil bacterial communities; however, bacteria are not the only microorganisms found in soil. To our knowledge, no study has compared the diversities of the four major microbial taxa, i.e., bacteria, archaea, fungi, and viruses, from an individual soil sample. We used metagenomic and small-subunit RNA-based sequence analysis techniques to compare the estimated richness and evenness of these groups in prairie, desert, and rainforest soils. By grouping sequences at the 97% sequence similarity level (an operational taxonomic unit [OTU]), we found that the archaeal and fungal communities were consistently less even than the bacterial communities. Although total richness levels are difficult to estimate with a high degree of certainty, the estimated number of unique archaeal or fungal OTUs appears to rival or exceed the number of unique bacterial OTUs in each of the collected soils. In this first study to comprehensively survey viral communities using a metagenomic approach, we found that soil viruses are taxonomically diverse and distinct from the communities of viruses found in other environments that have been surveyed using a similar approach. Within each of the four microbial groups, we observed minimal taxonomic overlap between sites, suggesting that soil archaea, bacteria, fungi, and viruses are globally as well as locally diverse.

The diversity and biogeography of soil bacterial communities

For centuries, biologists have studied patterns of plant and animal diversity at continental scales. Until recently, similar studies were impossible for microorganisms, arguably the most diverse and abundant group of organisms on Earth. Here, we present a continental-scale description of soil bacterial communities and the environmental factors influencing their biodiversity. We collected 98 soil samples from across North and South America and used a ribosomal DNA-fingerprinting method to compare bacterial community composition and diversity quantitatively across sites. Bacterial diversity was unrelated to site temperature, latitude, and other variables that typically predict plant and animal diversity, and community composition was largely independent of geographic distance. The diversity and richness of soil bacterial communities differed by ecosystem type, and these differences could largely be explained by soil pH (r(2) = 0.70 and r(2) = 0.58, respectively; P < 0.0001 in both cases). Bacterial diversity was highest in neutral soils and lower in acidic soils, with soils from the Peruvian Amazon the most acidic and least diverse in our study. Our results suggest that microbial biogeography is controlled primarily by edaphic variables and differs fundamentally from the biogeography of "macro" organisms.