Bacterial diversity and enzymatic activity in a soil recently treated with tebuconazole

Dependence of soil microbial community structure and function on land use types and management regimes

Changes in altitude can cause regional microclimate changes, leading to the spatial heterogeneity of environmental factors and soil bacteria. However, the internal driving process and mechanism remain unclear. Here, we selected Fanjingshan, a typical nature reserve in the subtropical region of south China with a clear altitudinal belt, to reveal the response mechanisms of microbial populations with altitude changes. We examined the physiochemical and biological properties (pH and soil enzyme activities) of 0~10 cm soil layers, soil bacterial diversity, and community structure across the 2.1 km belt (consisting of six altitude ranges). Our results showed that soil pH was highest at the altitude range below 900 m and decreased with altitude thereafter. Soil enzyme activities showed an overall decreasing trend with altitude rising. The soil sucrase and catalase activity was highest (48.35 mg.g-1.d-1 and 23.75 µmol.g-1, respectively) at altitudes below 900 m; the soil urease activity was highest (704.24 µg.g-1.d-1) at 900~1200 m; and the soil acid phosphatase activity was highest (57.18 µmol.g-1) at 1200~1500 m. In addition, the soil bacterial community diversity showed a linear increasing trend, with the maximum abundance at 1500~1800 m. Soil pH was correlated with enzyme activity and bacterial community composition and structure, and the correlation was the strongest between pH and the distribution of bacterial diversity at altitudes below 900 m. Overall, soil enzyme activities and soil bacterial diversity showed spatial heterogeneity along the altitude gradient, and their community structure and composition were affected by altitude as a result of changes in soil physicochemical factors. This study provides a better and deeper understanding of the spatial succession of soil in the Fanjingshan area and the distribution pattern of soil microorganisms in central subtropical mountain ecosystems.

Aluminum is a major deleterious factor for soybean productivity in acidic soils. Soil enzyme activities and bacteria play important roles in improving the stress tolerance of soybean. We assessed soil enzyme activities and bacterial structure and functions in Al-tolerant (Al-T) and Al-sensitive (Al-S) soybean genotypes subjected to different Al stress. We used a pot experiment system and determined plant biomass, urease, acid phosphatase, catalase, sucrase, and amylase activities, soil chemical properties, and the rhizosphere bacterial community diversity and structure of Al-T and Al-S soybean genotypes under different Al concentrations (0, 0.2, and 0.4 Al3+ g kg−1). Significant differences in soil enzyme activities and bacterial community structure were only observed between Al-T and Al-S soybeans under high Al stress. We identified 23 operational taxonomic units (OTUs), including OTU46 (Tumebacillus), OTU253 (Granulicella), and OTU180 (Burkholderia), which may improve soybean tolerance to Al toxicity. The results of canonical correspondence analysis (CCA) indicated that NH4+-N was an important factor that drove bacterial community structure differences between the two genotypes. Al stress simplified the network structure in the Al-T soybean, which may cause the soil bacterial community to be easily influenced by biotic and abiotic factors. High Al stress drove different soil enzyme activities and bacterial community structures between Al-T and Al-S soybean genotypes, and NH4+-N was the most important factor that drove the bacterial community structure between the two genotypes. Al-T soybeans recruited Al-tolerant microorganisms, such as Tumebacillus, Granulicella, and Burkholderia, to improve the resistance to Al stress. Nevertheless, Al stress simplified the network structure in the Al-T soybeans, which may allow for the soil bacterial community to be easily influenced by other biotic and abiotic factors.

Current Australian legislation permits the beneficial application of grease trap waste (GTW) to agricultural soil, viewing it as a beneficial source of organic matter and soil conditioner containing no/low amounts of metals or pathogenic organisms. However, little is known about the influence of GTW on soil bacterial community. A field experiment was established at Menangle in south western Sydney in Australia to quantitatively assess the impacts of different types (GTW CO and GTW CL) and amounts of GTW application on the soil bacterial community and diversity. Furthermore, a municipal solid waste (MSW) compost was simultaneously examined to compare against the other organic wastes. Knowledge about the shifts in microbial community structure and diversity following the applications of organic wastes could help to evaluate the ecological consequences on the soil and thus to develop sound regulatory guidelines for the beneficial reuse of organic wastes in agricultural lands. Soil samples were collected from recycled organics plots treated with different types and quantity of organic wastes. The field experimental treatments included control (CK, without application of any organic wastes), low amount of GTW CO (COL), GTW CL (CLL), and MSW (ML), and high amounts of GTW CO (COH), GTW CL (CLH), and MSW compost (MH). Microbial DNA was extracted from soil samples and the 16S rRNA genes were polymerase chain reaction (PCR)-amplified. The PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), cloning, and sequencing. The bacterial community structures and diversity were assessed using the DGGE profiles and clone libraries constructed from the excised DGGE bands. DGGE-based analyses showed that application of the GTW CO, regardless of the amount applied, had significant negative effects on soil bacterial genotypic diversity and community structure compared with the control, while the applications of other organic wastes including the GTW CL and MSW had no clear effects. The effects of the rate of organic waste application on soil bacterial community characteristics varied with the types of organic wastes applied. Sequence-based analyses of 126 clones indicated that Proteobacteria (53.2%) was the dominant taxa at the experimental site, followed by Actinobacteria (9.5%), Bacteroidetes (7.9%), Firmicutes (7.9%), Gemmatimonadetes (5.6%), Chloroflexi (2.4%), Acidobacteria (1.6%) and the unclassified group (11.9%). In the COH treatment, Acidobacteria, Bacteroidetes, and Gemmatimonadetes were not detected; the percentages of Firmicutes, Proteobacteria, and Actinobacteria in the COH treatment were significantly different from those in CK. There is a significant positive correlation (r = 0.71, p = 0.002) between the C/N ratio of organic wastes and the bacterial genotypic communities. Both the type and the amount of GTW applied affected soil bacterial genotypic diversity and community structure. The different effects of various types of organic wastes on soil bacterial characteristics may be predicted by the differences in specific properties of organic wastes such as C/N ratio, as evidenced by the strong and significant positive relationship between the bacterial community distance and the environmental distance of C/N ratio. This also indicates that the C/N ratio of GTW applied can be a major driver for the shift in the soil bacterial community. Our results revealed that the effects of organic wastes on soil bacterial communities varied with the types of organic wastes, and depending on the rate of application. Application of the GTW CO led to significant shifts in soil bacterial community diversity and structure. The effects of different types of organic wastes on the soil bacterial characteristics can be predicted by the differences of specific properties of organic wastes, such as the C/N ratio. Sequence-based analyses of 126 clones indicated that Proteobacteria was the dominant taxa at the experimental site. Our results have important implications for developing sound regulatory guidelines for the beneficial reuse of organic wastes, indicating that GTW CO and similar organic waste treatments may not be suitable for application in agricultural soils due to its significant negative effect on soil bacterial community.

Heavy metal pollution poses a serious hazard to the soil bacterial community. In this study, the 16 s rRNA high-throughput sequencing technology was used to analyze bacterial diversity and structure of dry field soil at different levels of heavy metal pollution. Further, the relationships between soil parameters and bacterial community were analyzed. Based on the study findings, we classified the levels of heavy metal pollution in soil samples from the study area could be divided into four grades: high risk (HR), considerable risk (CR), moderate risk (MR) and low risk (LR). In this study, heavy metal concentrations and pH showed significant effect on bacterial community structure. The distribution of bacterial community richness and diversity was MR > LR > CR > HR. Bacterial communities such as Acidobacteria, Chloroflexi and Gemmatimonadetes were highly resistant to the lower pH (pH < 6.5) and the high levels of heavy metal pollution compared with other bacterial community, which were abundant in HR samples. However, Proteobacteria, Actinobacteria, Bacteroidetes and Latescibacteria were more abundant in alkaline soils (pH > 7.5). Further, available Cd, Pb and Zn concentrations were lower in alkaline soils than acidic soils, which reduced the impact of heavy metals on bacterial community diversity and structure.

The goals of the study were to assess the diversity and structure of the bacterial communities within the soil depth along a gradient of heavy metal (HM) contamination and to identify indigenous bacterial species in the agricultural area of a non-ferrous metal plant KCM 2000 Group (Plovdiv) by using 16S rRNA gene retrieval. 16S rRNA gene clone libraries were constructed for nine samples, which were collected from two soil depths in June 2020. From each library, up to 100 clones were analysed and grouped into operational taxonomic units (OTUs) by restriction fragment length polymorphism (RFLP). The representatives of the OTUs were sequenced, followed by phylogenetic analysis. The results revealed that phyla Proteobacteria (11.11–71.43%) and Actinomycetota (3.57–33%) were the most abundant. Surface soils (12 phyla and 15 classes) were more diverse than subsurface ones (7 phyla and 12 classes). The lowest diversity at both phylum and class levels was calculated for the moderately contaminated soils from the two studied depths. Thirteen 16S rDNA sequences were identified to a species level, and they belonged to Proteobacteria, Actinomycetota and Firmicutes. This study highlighted that both HM contamination and soil depth caused shifts in diversity and structure of soil bacterial communities.

Alkaline lakes are a special aquatic ecosystem that act as important water and alkali resource in the arid-semiarid regions. The primary aim of the study is to explore how environmental factors affect community diversity and structure, and to find whether there are key microbes that can indicate changes in environmental factors in alkaline lakes. Therefore, four sediment samples (S1, S2, S3, and S4) were collected from Hamatai Lake which is an important alkali resource in Ordos’ desert plateau of Inner Mongolia. Samples were collected along the salinity and alkalinity gradients and bacterial community compositions were investigated by Illumina Miseq sequencing. The results revealed that the diversity and richness of bacterial community decreased with increasing alkalinity (pH) and salinity, and bacterial community structure was obviously different for the relatively light alkaline and hyposaline samples (LAHO; pH < 8.5; salinity < 20‰) and high alkaline and hypersaline samples (HAHR; pH > 8.5; salinity > 20‰). Firmicutes, Proteobacteria and Bacteriodetes were observed to be the dominant phyla. Furthermore, Acidobacteria, Actinobacteria, and low salt-tolerant alkaliphilic nitrifying taxa were mainly distributed in S1 with LAHO characteristic. Firmicutes, Clostridia, Gammaproteobacteria, salt-tolerant alkaliphilic denitrifying taxa, haloalkaliphilic sulfur cycling taxa were mainly distributed in S2, S3 and S4, and were well adapted to haloalkaline conditions. Correlation analysis revealed that the community diversity (operational taxonomic unit numbers and/or Shannon index) and richness (Chao1) were significantly positively correlated with ammonium nitrogen (r = 0.654, p < 0.05; r = 0.680, p < 0.05) and negatively correlated with pH (r = −0.924, p < 0.01; r = −0.800, p < 0.01; r = −0.933, p < 0.01) and salinity (r = −0.615, p < 0.05; r = −0.647, p < 0.05). A redundancy analysis and variation partitioning analysis revealed that pH (explanation degrees of 53.5%, pseudo-F = 11.5, p < 0.01), TOC/TN (24.8%, pseudo-F = 10.3, p < 0.05) and salinity (9.2%, pseudo-F = 9.5, p < 0.05) were the most significant factors that caused the variations in bacterial community structure. The results suggested that alkalinity, nutrient salt and salinity jointly affect bacterial diversity and community structure, in which one taxon (Acidobacteria), six taxa (Cyanobacteria, Nitrosomonadaceae, Nitrospira, Bacillus, Lactococcus and Halomonas) and five taxa (Desulfonatronobacter, Dethiobacter, Desulfurivibrio, Thioalkalivibrio and Halorhodospira) are related to carbon, nitrogen and sulfur cycles, respectively. Classes Clostridia and Gammaproteobacteria might indicate changes of saline-alkali conditions in the sediments of alkaline lakes in desert plateau.

Soil pH and nutrients shape the vertical distribution of microbial communities in an alpine wetland

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).

Diversity and Ecology of the Roseobacter Clade and other Marine Microbes as revealed by Metagenomic and Metatranscriptomic Approaches

Effects of living mulches on the soil nutrient contents, enzyme activities, and bacterial community diversities of apple orchard soils

Structure of the epiphytic bacterial communities of Macrocystis pyrifera in localities with contrasting nitrogen concentrations and temperature

Soil microorganisms play a key role in soil physical structure. Soil microbial community structure and functions are in turn affected by soil aggregation or degradation. The objectives of this study were to determine the impact of (1) soil aggregate-size distribution and (2) soil compaction on bacterial community richness and structure under three intensive potato (Solanum tuberosum) cropping systems. In June and July 2014, soil samples were collected at a depth of 0-20 cm from 16 sites in Quebec, Canada. The samples were analyzed for aggregate-size distribution, particle-size distribution, total carbon, total nitrogen, total sulfur, oxalate-extractable potassium and phosphorus, gravimetric moisture content, pH and degree of compactness (DC). Soil bacterial community diversity was assessed by using the high-throughput sequencing Illumina MiSeq platform to target the V6-V8 region of bacterial 16S rRNA gene. Bacterial alpha diversity and community structure were found to be affected by cropping systems. Faith's phylogenetic diversity index and bacterial richness increased with increasing proportions of the 1–0.5 mm and 2–1 mm aggregate-size fractions and micro-aggregates in soils. Redundancy analysis revealed a strong correlation between soil bacterial community structure and soil aggregate-size distribution. Eight of the 27 dominant bacterial classes had a significant relationship with aggregate size fractions >2 mm, 1- 0.5 mm and < 0.1 mm. In addition, the degree of soil compaction had a significant effect on soil bacterial community structure, with 70% of the dominant classes showing greater relative abundance in the moderate and high DC groups than in the low DC group. This research provided a benchmark for bacterial community structure in potato agroecosystems as impacted by soil aggregation and compaction.

It has been shown that the golden apple snail (GAS, Pomacea canaliculata), which is a serious agricultural pest in Southeast Asia, can provide a soil amendment for the reversal of soil acidification and degradation. However, the impact of GAS residue (i.e., crushed, whole GAS) on soil bacterial diversity and community structure remains largely unknown. Here, a greenhouse pot experiment was conducted and 16S rRNA gene sequencing was used to measure bacterial abundance and community structure in soils amended with GAS residue and lime. The results suggest that adding GAS residue resulted in a significant variation in soil pH and nutrients (all P < 0.05), and resulted in a slightly alkaline (pH = 7.28–7.75) and nutrient-enriched soil, with amendment of 2.5–100 g kg−1 GAS residue. Soil nutrients (i.e., NO3-N and TN) and TOC contents were increased (by 132–912%), and some soil exocellular enzyme activities were enhanced (by 2–98%) in GAS residue amended soil, with amendment of 1.0–100 g kg−1 GAS residue. Bacterial OTU richness was 19% greater at the 2.5 g kg−1 GAS residue treatment than the control, while it was 40% and 53% lower at 100 g kg−1 of GAS residue and 50 g kg−1 of lime amended soils, respectively. Firmicutes (15–35%) was the most abundant phylum while Bacterioidetes (1–6%) was the lowest abundant one in GAS residue amended soils. RDA results suggest that the contents of soil nutrients (i.e., NO3-N and TN) and soil TOC explained much more of the variations of bacterial community than pH in GAS residue amended soil. Overuse of GAS residue would induce an anaerobic soil environment and reduce bacterial OTU richness. Soil nutrients and TOC rather than pH might be the main factors that are responsible for the changes of bacterial OTU richness and bacterial community structure in GAS residue amended soil.

Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depth-related patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depth-related variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO(3)(-), indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.