Relative Abundance Of Gemmatimonadetes Research Articles

Effects of Biochar-loaded Ammonia Nitrogen on Soil Carbon Emissions, Enzyme Activity, and Microbial Communities

The form of soil nitrogen input significantly affects soil CO2 emission. As a new form of nitrogen input, biochar-loaded ammonia nitrogen not only reduces the input of chemical nitrogen fertilizer in farmland but also reduces the cost of environmental treatment. It is of great significance to promote the zero growth of national chemical fertilizer, the prevention and control of farmland non-point source pollution, and the realization of the national goal of "carbon peak" and "carbon neutralization." Through an indoor culture experiment, the effects of different nitrogen input forms on soil carbon emission, enzyme activity, and microbial community were studied through four treatments:no fertilization (CK), single application of chemical nitrogen fertilizer (CF), biochar combined application of chemical nitrogen fertilizer (BF), and biochar-loaded ammonia nitrogen (BN). The results showed that compared with that in CF, BF significantly increased cumulative carbon emissions (66.24 %), whereas BN had no significant difference. It is worth noting that the cumulative carbon emissions were significantly reduced by 35.28 % compared with that in BF and BN. Compared with those in CF and BF, the activities of β-glucosidase, peroxidase, and polyphenol oxidase treated with BN significantly increased by 20.25 % and 5.20 %, respectively. Compared with that in CF, the BF treatment increased microbial community richness and community diversity, whereas the BN treatment decreased microbial community richness. Compared with that in BF, the relative abundance of Proteobacteria decreased by 11.16 %, and the relative abundance of Actinobacteria and Bacteroidota increased by 8.12 % and 5.83 %, respectively, in which xylosidase activity was the most important soil factor affecting microbial community structure. The relative abundance of Chloroflexi was significantly correlated with cellobiose hydrolase activity, and the relative abundance of Gemmatimonadetes was significantly correlated with β-glucosidase activity. There was a very significant correlation between the relative abundance of Proteobacteria and cumulative carbon emissions. To summarize, compared with those under biochar combined with chemical nitrogen fertilizer, biochar loaded with ammonia nitrogen significantly reduced cumulative carbon emissions, and its emission reduction effect was better. The results of this study will be beneficial to the landing of the national "double carbon strategy," the healthy development of the biological natural gas industry, the construction of the national green cultivation circular agriculture system, and the realization of the national zero growth strategy of chemical fertilizer.

Effects of short‐term nitrogen addition on rhizosphere and bulk soil bacterial community structure of three halophytes in the Yellow River Delta

AbstractThe total amount and rate of atmospheric nitrogen (N) deposition are constantly increasing, which substantially influences the soil microbial community structure and function. However, it is still unclear whether the responses of different plant rhizosphere soil bacterial community to short‐term N addition was consistent. Based on 16s rRNA sequencing, we investigated the responses of rhizosphere and bulk soil bacterial community of halophytes (salt‐absorbing, salt‐rejecting, and salt‐secreting plant) to short‐term N addition in the Yellow River Delta. The bacterial community α‐diversity of Suaeda salsa (salt‐absorbing plant) was significantly higher in rhizosphere soil than in bulk soil, while no significant difference between Phragmites communis (salt‐rejecting plant) rhizosphere and bulk soil bacterial community α‐diversity was found. The differences were mainly ascribed to the higher N uptake capacity of P. communis, which resulted in no difference in N content between rhizosphere and bulk soil. The short‐term N addition significantly increased the α‐diversity of bacterial community in the rhizosphere soil of Aeluropus sinensis (salt‐secreting plant), but there was no effect on the α‐diversity of bacterial community in the rhizosphere soil of P. communis. Nitrogen addition enhances the salt uptake capacity of A. sinensis and alleviates the salt stress of bacterial growth. The relative abundance of Bacteroidetes for S. salsa and A. sinensis was significantly higher in rhizosphere soil than in bulk soil, and the relative abundance of Actinobacteria for P. communis and S. salsa was higher and lower in rhizosphere soil than in bulk soil, respectively. Salt‐absorbing of S. salsa leads to elevated rhizosphere soil salinity. Higher salinity and abundant carbon promote the Bacteroidetes and inhibit the Actinobacteria. Short‐term N addition caused an increase in the relative abundance of Gemmatimonadetes in halophyte rhizosphere soil and a decrease in the relative abundance of Firmicutes in S. salsa and A. sinensis bulk soil, which may be due to the different response of C:N of root secretions to N addition in halophytes. The relative abundance of rhizosphere soil denitrifying bacteria was higher in S. salsa and A. sinensis than in P. communis, while the reverse was observed for N‐fixing bacteria. The relative abundance of denitrifying bacteria decreased in P. communis and increased in S. salsa and A. sinensis. The low N soil environment of P. communis promotes the activity of N‐fixing bacteria, and the abundant N content of S. salsa and A. sinensis soil promotes the denitrification process. The research clarified that the response of soil bacterial community to short‐term N addition Treatment differed due to the influence of plant species and that N additions had smaller effects on the bacterial community than plant species.

Differential Response of Soil Microbial Community Structure in Coal Mining Areas during Different Ecological Restoration Processes

Micro-organisms play important roles in promoting soil ecosystem restoration, but much of the current research has been limited to changes in microbial community structure in general, and little is known regarding the more sensitive and indicative microbial structures or the responses of microbial diversity to environmental change. In this study, based on high-throughput sequencing and molecular ecological network analyses, the structural characteristics of bacterial communities were investigated in response to four different ecological restoration modes in a coal mining subsidence area located in northwest China. The results showed that among soil nutrients, nitrate-nitrogen and fast-acting potassium were the most strongly associated with microbial community structure under different ecological restoration types. Proteobacteria, Actinobacteria, and Acidobacteria were identified as important phyla regarding network connectivity and structural composition. The central natural recovery zone was found to have the smallest network size and low complexity, but high modularity and good microbial community stability. Contrastingly, a highly complex molecular ecological network of soils in the photovoltaic economic zone existed beneath the photovoltaic modules, although no key species, strong bacterial competition, poor resistance to disturbance, and a significant increase in the relative abundance of Gemmatimonadetes were found. Furthermore, the reclamation zone had the highest soil nutrient content, the most complex network structure, and the most key and indicator species; however, the ecological network was less stable and readily disturbed.

Bacterial community structure and diversity in the rhizospheric soil of Robinia pseudoacacia and Juniperus sabina planted in iron tailings matrix.

Iron tailings matrix is deficient in nutrients, and phytoremediation is one of the effective methods to improve tailings nutrients. The response of phytoremediation to tailings microorganisms remains to be studied. The present study analyzed rhizospheric soil of two kinds of plants bacterial diversity and community structure and their relationship with soil environmental factors. The results indicate that the rhizospheric soil bacteria species of Robinia pseudoacacia and Juniperus sabina were not significantly different from that of bare tailings, but rhizospheric soil bacterial community compositions and abundance were significantly different from that of bare tailings. Canonical correlation analysis (CCA) showed that soil alkali-hydrolyzable nitrogen (AN), soil total nitrogen (TN), and soil organic matter (SOM) were the main environmental factors affecting bacterial community diversity. Spearman's correlation analysis showed that AN, TN, and SOM were significantly positively correlated with the relative abundance of Gemmatimonadetes and Nitrospirae, and were significantly negatively correlated with that of Firmicutes, Fusobacteria, and Bacteroidetes. FAPROTAX function prediction showed that the functional microbial communities of rhizospheric soil of the two plants were significantly different from those of bare tailings. Overall, the findings support an increase of microbial diversity, SOM, and nitrogen in rhizospheric soil of revegetated tailings compared to bare tailings. These results provide theoretical support for the development and application of phytoremediation in abandoned mines.

Effect of Biochar on Soil Enzyme Activity & the Bacterial Community and Its Mechanism

Biochar-based fertilizers can improve the mineralization of carbon and nitrogen in soil and enhance the soil micro-ecological environment due to particular physical and chemical properties. It is of great significance to explore the underlying mechanism of biochar-based fertilizer in the regulation of soil microorganisms and soil enzyme activity to improve soil quality. Field experiments were conducted to investigate the effects of different biochar-based fertilizer rates[0 (CK2), 0.6 (T1), 0.9 (T2), 1.2 (T3), and 1.5 (T4) t·hm-2]on soil nutrients, soil enzyme activity, and bacterial community structure. The results showed that with the application of biochar-based fertilizer, soil bulk density decreased, while the pH value, available P, available K, organic matter content, and the C/N ratio increased by 0.32%-5.83%, 14.09%-23.16%, 0%-38.70%, 7.49%-14.16%, and 4.06%-10.13%, respectively, compared to that of the CK2 treatment. With increasing rates of biochar-based fertilizer, the enzyme activity first increased and then decreased. Invertase (INV), urease (URE), catalase (CAT), and neutral phosphatase (NPH) activity under the application of biochar-based fertilizer were 63.73%-166.37%, 117.52%-174.03%, 12.98%-23.59%, and 60.84%-119.71% higher than that of CK2, respectively. The corresponding bacterial diversity was significantly improved, especially with regard to the increase in the abundance of growth promoting bacteria, such as Gemmatimonadetes and Proteobacteria, and decreased the abundance of Acidobacteria and Actinobacteria. The correlation analysis showed that soil C/N ratio was the key factor affecting soil enzyme activity, and there was a significant positive correlation between soil enzyme activity and bacterial diversity. There were significantly positive correlations among the activities of the above four soil enzymes and the relative abundance of Gemmatimonadetes (P<0.01), with CAT being the key factor affecting the bacterial community structure. This study revealed a relationship between soil enzyme activity and microbial colonies, which provides a theoretical basis and mechanism for applying biochar to regulate the soil enzyme and micro-ecological environment.

Microbial diversity and activity assessment in a 100-year-old lead mine

Mining activities frequently leave a legacy of residues that remain in the area for long periods causing the pollution of surroundings. We studied on a 100 year-old mine, the behavior of potentially toxic elements (PTEs) and their ecotoxicological impact on activity and diversity of microorganisms. The PTEs contamination assessment allowed the classification of the materials as highly (reference- and contaminated-samples) and very highly polluted (illegal spill of olive mill wastes (OMW), tailings, and dumps). OMW presented the lowest enzymatic activities while tailings and dumps had low dehydrogenase and arylsulfatase activities. All the α-diversity indices studied were negatively impacted in dumps. Tailings had lower Chao1 and PD whole tree values as compared to those of reference-samples. β-diversity analysis showed similar bacterial community composition for reference- and contaminated-samples, significantly differing from that of tailings and dumps. The relative abundance of Gemmatimonadetes, Bacteroidetes, and Verrucomicrobia was lower in OMW, tailings, and dumps as compared to reference-samples. Fifty-seven operational taxonomic units were selected as responsible for the changes observed between samples. This study highlights that assessing the relationship between physicochemical properties and microbial diversity and activity gives clues about ongoing regulating processes that can be helpful for stakeholders to define an appropriate management strategy.

Response of Bacterial and Fungal Communities to Chemical Fertilizer Reduction Combined with Organic Fertilizer and Straw in Fluvo-aquic Soil

To investigate the effects of chemical fertilizer reduction combined with organic fertilizer and straw on bacterial and fungal communities in fluvo-aquic soil under a wheat-maize rotation system in North China, a field-oriented fertilization experiment was performed at a trial base in Ninghe District of Tianjin. The differences in composition, diversity, and structure of bacterial and fungal communities were evaluated using five fertilization patterns (chemical fertilizer, F; chemical fertilizer reduction, FR; chemical fertilizer reduction combined with straw, FRS; chemical fertilizer reduction combined with organic fertilizer, FRO; chemical fertilizer reduction combined with organic fertilizer and straw, FROS) using Illumina high-throughput sequencing technology. Further, the main soil environmental factors driving the alteration of bacterial and fungal communities under different fertilization treatments were explored in combination with soil chemical analysis. The results showed that adding organic fertilizer (FRO) significantly increased the SOM content. In comparison with the FRS treatment, the TP content in the FROS treatment significantly increased by 13.33%. The AP content increased significantly after applying the FRO and FROS treatment, and it increased by 18.03%-33.45% and 22.69%-38.72%, respectively, as compared to that with the other treatments. The NH4+-N content of FRO and FROS treatments was significantly higher than that of chemical fertilizer treatments (F and FR), which was 2.14 and 2.23 times that of F treatment, and 2.23 and 2.33 times that of FR treatment, respectively. Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria were the dominant bacterial phyla for all treatments, with Ascomycota being the dominant fungal phylum. Based on the chemical fertilizer reduction combined with organic fertilizer, the addition of straw (FROS) significantly decreased the relative abundance of Actinobacteria. Under the FRS and FROS treatments, a significant decrease in the relative abundance of Gemmatimonadetes was observed. Moreover, the FROS treatment caused a significant decrease in the relative abundance of Planctomycetes and Verrucomicrobia. As for the fungal community, the relative abundance of Ascomycota was significantly increased under the treatments applying organic fertilizer (FRO and FROS). In comparison with the FR treatment, the FROS treatment significantly decreased the relative abundance of Mortierellomycota and Olpidiomycota, and the FRS treatment also showed a significant inhibitory effect on the relative abundance of Mortierellomycota. The Shannon index of bacterial community of the FROS treatment was significantly reduced by 1.26% and 1.25% in comparison with the F and FR treatments, respectively; the Chao1 index increased by 4.51% as compared with that of the F treatment. The Shannon index of bacterial community exhibited a significantly positive correlation with available phosphorus as well as ammonium content (P<0.05). In comparison to the FR treatment, the FRS, FRO, and FROS treatments significantly decreased the Shannon index of fungal community by 29.85%, 24.94%, and 25.73%, respectively. A significantly positive relationship between the Shannon index of fungal community and available phosphorus content was observed. The community structure of bacteria of the FROS treatment was significantly different from that of F, FR, and FRO treatments, with the soil moisture, total phosphorus, pH, and available phosphorus as the major driving factors; the fungal community structure of the FRO and FROS treatments showed significant difference from that of the F and FR treatments, and the fungal community structure was mainly altered by total nitrogen, available phosphorus, and total phosphorus. In summary, our results indicated that the bacterial and fungal communities in fluvo-aquic soil exhibited a relatively strong response to the chemical fertilizer reduction combined with organic fertilizer and straw; meanwhile, the fungal community was also significantly influenced by chemical fertilizer reduction with organic fertilizer. Therefore, the organic fertilizer and straw drive the changes in the bacterial and fungal community composition, while improving the soil physicochemical properties. The fluvo-aquic fungi were more sensitive to the organic materials than the bacteria. Soil P was a common important influencing factor for regulating the bacterial and fungal community structure, and it should be paid full attention during the agricultural cultivation of fluvo-aquic soil.

Utilization of carbon sources in the rice rhizosphere and nonrhizosphere soils with different long-term fertilization management.

Carbon (C) plays an important role in the interaction between plant and rhizosphere microbial communities, but there is still limited information about how C source utilization soil microbial structure responds to soil fertility changes under the double-cropping rice (Oryza sativa L.) system in Southern China paddy fields. Therefore, the effects of long-term (33 years) fertilizer regimes on the characteristics of C utilization in both rhizosphere and nonrhizosphere soils under double-cropping rice fields in Southern China were investigated by using the metagenome sequencing technology. The experiment began in 1986, and included five fertilizer treatments: without fertilizer input (CK), chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic matter, and 70% chemical fertilizer (LOM), and 60% organic matter and 40% chemical fertilizer (HOM). The results showed that the relative abundance of Gemmatimonadetes and Planctomycetia in both the rhizosphere and nonrhizosphere soils was increased by application of rice straw residue and organic manure, whereas the relative abundance of Gammaproteobacteria and Nitrospira was promoted by application of inorganic fertilizers. The largest group of clusters of orthologous groups of proteins categories was "amino acid transport and metabolism" with 16.46% unigenes, followed by "general function prediction only" (12.23%). Regarding the gene ontology categories, biological process were the largest category (174 949, 46.40%), followed by cellular component (126 766, 33.62%), and molecular function (110 353, 29.26%). The principal coordinate analysis indicated that different parts of the root zone were the most important factors affecting the variation of C source utilization bacteria community, and the different fertilizer treatments were the second important factor affecting the variation of C source utilization bacteria community. As a result, the application of fertilization practices had significant effects on the abundance and community composition of C source utilization microbes in paddy soils. The results showed that the combined application of rice straw residue or organic manure with chemical fertilizer practices significantly increases the C source utilization of soil microorganisms in double-cropping rice fields.

The Bacterial Community Structure and Microbial Activity in a Traditional Organic Milpa Farming System Under Different Soil Moisture Conditions.

Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, i.e., inorganic fertilization, tillage, crop residue removal and maize (Zea mays L.) monoculture, and traditional organic farmed soil “milpa,” i.e., minimum tillage, rotation of maize, pumpkin (Cucurbita sp.) and beans (Phaseolus vulgaris L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5%FC, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5%FC, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.

Effects of permafrost collapse on soil bacterial communities in a wet meadow on the northern Qinghai-Tibetan Plateau

BackgroundPermafrost degradation may develop thermokarst landforms, which substantially change physico–chemical characteristics in the soil as well as the soil carbon stock. However, little is known about changes of bacterial community among the microfeatures within thermokarst area.ResultsWe investigated bacterial communities using the Illumina sequencing method and examined their relationships with soil parameters in a thermokarst feature on the northern Qinghai-Tibetan Plateau. We categorized the ground surface into three different micro-relief patches based on the type and extent of permafrost collapse (control, collapsing and subsided areas). Permafrost collapse significantly decreased the soil carbon density and moisture content in the upper 10 cm samples in the collapsing areas. The highest loading factors for the first principal component (PC) extracted from the soil parameters were soil carbon and nitrogen contents, while soil moisture content and C:N ratios were the highest loading factors for the second PC. The relative abundance of Acidobacteria decreased with depth. Bacterial diversity in subsided areas was higher than that in control areas.ConclusionsBacterial community structure was significantly affected by pH and depth. The relative abundance of Gemmatimonadetes and Firmicutes were significantly correlated with the first and second PCs extracted from multiple soil parameters, suggesting these phyla could be used as indicators for the soil parameters in the thermokarst terrain.

Microbial diversity and community structure in agricultural soils suffering from 4 years of Pb contamination.

Heavy metal pollution has become a widespread environmental problem due to rapid economic development. The phylogenetic diversity and structure of microbial communities in lead (Pb)-contaminated Lou soils were investigated using Illumina MiSeq sequencing of 16S rRNA genes. The presence of Pb2+ in soil showed weak impact on the diversity of soil bacteria community, but it influenced the abundance of some genera of bacteria, as well as soil physicochemical properties. We found significant differences in the relative abundances of heavy-metal-resistant bacteria such as Bacillus, Streptococcus, and Arthrobacter at the genus level. Available Pb and total Pb negatively correlated with soil organic matter but positively affected available phosphorus. The abundance of main bacteria phyla was highly correlated with total Pb. The relative abundance of Gemmatimonadetes, Nitrospirae, and Planctomycetes was negatively correlated with total Pb. Collectively, Pb influences both the microbial community composition and physicochemical properties of soil.