Microbial Functional Diversity Research Articles

Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere.

Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.

Enzyme activities and microbial functional diversity in metal(loid) contaminated soils near to a copper smelter.

The monitoring of soil metal(loid) contamination is of global significance due to deleterious effects that metal(loid)s have on living organisms. Soil biological properties such as enzyme activities (EAs) are good indicators of metal(loid) contamination due to their high sensitivity, fast response, and low-cost. Here, the effect of metal(loid) contamination on physicochemical properties and microbial functionality in soils sampled from within 10km of a Cu smelter is investigated. Soil composite samples were randomly taken within 2, 4, 6, 8 and10km zones from a mining industry Cu smelter. The EAs of dehydrogenase (DHA), arylsulfatase (ARY), β-glucosidase, urease, and arginine ammonification (AA) were studied as indicators of metal(loid) contamination, which included the ecological dose (ED50) with respect to Cu and As contents. The community level physiological profile (CLPP), functional diversity, and catabolic evenness were evaluated based on the C-substrate utilisation. All EAs decreased in zones with high degrees of metal(loid) contamination, which also had low TOC and clay contents, reflecting long term processes of soil degradation. Positive and strong relationships between EAs and TOC were found. DHA and ARY activities decreased by approximately 85-90% in highly metal(loid) contaminated soils. DHA and AA showed significant ED50 values associated with available Cu (112.8 and 121.6mg CuDTPA kg-1, respectively) and total As contents (30.8 and 31.8mg As kg-1, respectively). The CLPP showed different metabolic profiles along the metal(loid) contamination gradients. Long-term stress conditions in soils close to industrial areas resulted in the decreasing of general biological activity, catabolic capacity, and functional diversity.

Coupled biodegradation of p-nitrophenol and p-aminophenol in bioelectrochemical system: Mechanism and microbial functional diversity

Biodegradation mechanisms and microbial functional diversity during coupled p-nitrophenol (PNP) and p-aminophenol (PAP) degradation were studied in a bioelectrochemical system. PNP in the biocathode and PAP in the bioanode were almost completely removed within 28hr and 68hr respectively. The degradation followed the steps including hydrating hydroxyalkylation, dehydrogenating carbonylation, and hydrolating ring cleavage, etc. Metagemomic analysis based on the KEGG and eggNOG database annotations revealed the microbial composition and functional genes/enzymes related to phenol degradation in the system. The predominant bacteria genera were Lautropia, Pandoraea, Thiobacillus, Ignavibacterium, Truepera and Hyphomicrobium. The recognized biodegradation genes/enzymes related to pollutant degradation were as follows: pmo, hbd, & ppo for phenol degradation, nzba, amie, & badh for aromatic degradation, and CYP & p450 for xenobiotics degradation, etc. The co-occurrence of ARGs (antibiotic resistant genes), such as adeF, MexJ, ErmF, PDC-93 and Escherichia_coli_mdfA, etc., were annotated in CARD database during the biodegradation process. The Proteobacteria & Actinobacteria phylum was the primary host of both the biodegradation genes & ARGs in this system. The microbial functional diversity ensured the effective biodegradation of the phenol pollutants in the bioelectrochemical system.

Study on the relationship between bacterial wilt and rhizospheric microbial diversity of flue-cured tobacco cultivars

Bacterial wilt caused by Ralstonia solanacearum, is one of the serious soil-borne diseases in flue-cured tobacco production areas in China. However, it was found that the occurrence of bacterial wilt not only varied with different cultivars but also varied with various sites even under the condition of planting the same variety. It suggests that the occurrence of bacterial wilt could be controlled by regulating soil microorganism and the growth environment. Therefore, the relationship between microorganism’s diversity in the rhizosphere and actual incidences were evaluated on the number of symptomatic plants and the functional diversity of soil microorganisms in field trials on two sites. The results showed that the incidence of bacterial wilt in the same cultivar was varied between the two experimental sites. However, the same trend was found in the number of rhizospheric microbes among the three varieties except for fungi. Also, a good relationship was found between the number of pathogens, microbial functional diversity in the rhizosphere, and actual incidences. The utilization intensity of carbohydrates, amino acids, carboxylic acids, polymers, amines, and carbon utilization of rhizospheric soil microbial community was negatively related with the occurrence of bacterial wilt while it was on the opposite for the utilization intensity of phenolic acids. The results revealed that the mechanism for resistance in flue-cured tobacco was directly associated with the number of pathogenic microorganisms in rhizosphere and the diversity of rhizospheric microbes. By improving the diversity of rhizospheric microbes, the incidence of tobacco bacterial wilt disease can be reduced.

Tree species richness and water availability interact to affect soil microbial processes

The objective of this study was to examine the interactive influence of tree diversity and water availability on microbial functioning in surface soil (0–10 cm). The study was conducted at two field experiments (ages 4.2 and 9.0 years, respectively) of the TreeDivNet platform that established plantations with a gradient of tree species richness exposed to high and low water availability treatments. Soil microbial biomass, activity, functional diversity and functional identity were estimated using the MicroResp™ method. Soil organic carbon and several other variables potentially associated with soil processes (soil moisture, soil and air temperature, soil pH, soil C:N ratio, tree biomass) were also measured. Our results indicate that tree species richness significantly increased soil microbial biomass and, to a lesser extent, soil microbial activity in the high water availability treatment, at both trial sites. However, tree species richness effects on microbial processes were not expressed in the low water availability treatment, contrary to the stress-gradient hypothesis. Tree species richness and water treatment interaction impacted microbial biomass and activity through their effects on microbial functional diversity and identity at one site and air temperature at the other site. In conclusion, the mechanisms through which tree diversity creates bottom-up effects on biological soil processes depend on environmental conditions and time following the establishment of tree communities. Future research relating diversity and water availability effects on soil microbial processes should consider functional traits of tree species and a larger range of trophic levels including herbivores and soil fauna to better understand biodiversity-soil ecosystem function relationships in forest ecosystems.

Large-scale evidence for microbial response and associated carbon release after permafrost thaw.

Permafrost thaw could trigger the release of greenhouse gases through microbial decomposition of the large quantities of carbon (C) stored within frozen soils. However, accurate evaluation of soil C emissions from thawing permafrost is still a big challenge, partly due to our inadequate understanding about the response of microbial communities and their linkage with soil C release upon permafrost thaw. Based on a large-scale permafrost sampling across 24 sites on the Tibetan Plateau, we employed meta-genomic technologies (GeoChip and Illumina MiSeq sequencing) to explore the impacts of permafrost thaw (permafrost samples were incubated for 11days at 5°C) on microbial taxonomic and functional communities, and then conducted a laboratory incubation to investigate the linkage of microbial taxonomic and functional diversity with soil C release after permafrost thaw. We found that bacterial and fungal α diversity decreased, but functional gene diversity and the normalized relative abundance of C degradation genes increased after permafrost thaw, reflecting the rapid microbial response to permafrost thaw. Moreover, both the microbial taxonomic and functional community structures differed between the thawed permafrost and formerly frozen soils. Furthermore, soil C release rate over five month incubation was associated with microbial functional diversity and C degradation gene abundances. By contrast, neither microbial taxonomic diversity nor community structure exhibited any significant effects on soil C release over the incubation period. These findings demonstrate that permafrost thaw could accelerate C emissions by altering the function potentials of microbial communities rather than taxonomic diversity, highlighting the crucial role of microbial functional genes in mediating the responses of permafrost C cycle to climate warming.

Soil aggregate size-dependent relationships between microbial functional diversity and multifunctionality

Soil stability and aggregates are important drivers of soil fertility and microbial diversity and are highly vulnerable to land degradation. However, the role of soil aggregates in driving the responses of microbial functional diversity and multiple ecosystem services and functions (multifunctionality) to further degradation (e.g., fertilization) remains largely unexplored and poorly understood. In this study, we used soils from long-term experiments involving inorganic and organic fertilization treatments to investigate the role soil aggregates (microscale) play in driving microbial functional gene diversity (via GeoChip) and the activity of multiple extracellular enzymes in an agricultural ecosystem. We found that microbial functional gene diversity has a significant and positive relationship with soil multifunctionality, which is enhanced in soil aggregates by organic fertilizer but is reduced by inorganic fertilizer. We also found that soil aggregate fractions indirectly controlled multiple ecosystem functions via changes in functional diversity. Smaller soil aggregates with higher resource availability (carbon and nitrogen) supported more ecological functions than larger aggregates under contrasting fertilizer management regimes. Soil multifunctionality is regulated by the differences in resource availability and not by microbial functional gene composition, which suggests that microbial functional diversity contributed more to multifunctionality than gene composition. Random forest analysis and structural equation modeling indicated that soil carbon and nitrogen and microbial functional diversity together determined the multifunctionality, whereas soil traits have more standardized total effects than functional diversity. Our study highlights that soil aggregation stratifies soil nutrition and microbial functional diversity, which leads to the differentiation of aggregate ecosystem multifunctionality.

Microbial structure and function diversity of open dumpsite compost used as fertilizer by peasant farmers

A study was carried out to assess the microbial communities and functions in addition to several key environmental variables (pH, temperature, carbon, nitrogen, carbon to nitrogen ratio, and moisture) of open dumpsite compost. Sampling was done on days 45 and 90 following composting of the organic fraction of the municipal solid waste (MSW). Following community DNA extraction, sequencing was done on Illumina Miseq platform. Pair-ends of the sequences reads were assembled using the make-contigs tool while open reading frame (ORFs) was done using FragGeneScan and these were functionally annotated to several bioinformatics pipelines. Structural composition revealed 5 kingdoms namely bacteria, protozoa, unknown, archaea, and fungi but with varying degree of abundance. After unknown phyla, proteobacteria was the second dominant phyla with abundance of 42.45 and 40.30% , respectively on days 45 and 90 and they were well represented in the class, order and family taxas in both samples. Majority of the genus in both samples were uncultured genus. However, potential pathogenic species belonging to the genuses Clostridium, Escherichia, Pseudomonas, Enterococcus, Micrococcus, Shigella, Klebsiella and Bacillus amongst other were detected in our samples on 90days. Physiological diversity assessment revealed that carbohydrate (CHO) metabolisms were the most dominant and was almost similar in both samples. At day 45, the CHO metabolisms were dominated by phylotypes belonging to the alphaproteobacteria and betaproteobacteria classes of bacteria but it was more diverse on day 90 as Chlorobi, Gammaproteobacteria, Firmicutes, Actinobacteria, Tenericutes, and Planctomycetes were also involved. Other metabolisms such as amino acid, nucleotides, vitamins and co-factors, xenobiotics, genetic information and well as environmental information processing were also captured. This practice should be discouraged to avoid incidence of food-borne diseases.

Effect of High Temperature Film Mulching on Soil Microbial Functional Diversity by High Throughput Sequencing

Effect of High Temperature Film Mulching on Soil Microbial Functional Diversity by High Throughput Sequencing

凋落物对土壤有机碳与微生物功能多样性的影响

凋落物对土壤有机碳与微生物功能多样性的影响

氮磷添加和栽植密度对大叶相思林土壤微生物群落功能多样性的影响

土壤微生物群落是土壤质量潜在的生态指标，在维持生态系统功能和服务中起着关键的作用。采用Biolog-ECO微平板法，探讨氮磷添加与不同栽植密度交互对大叶相思林（Acacia auriculiformis）土壤微生物功能多样性的影响，以便为建立合理的林分密度和氮磷施肥模式，提高土壤质量提供理论参考。以大叶相思林为研究对象，选择氯化铵（NH₄Cl）作为氮肥模拟大气氮沉降，用二水合磷酸二氢钠（NaH₂PO₄·2H₂O）进行磷添加。氮磷处理设置4个水平，即CK、施N、施P和施N+P。种植密度设置4个水平，即1667、2500、4444、10000株/hm²（分别以低密度、中密度、较高密度、高密度表示）。研究结果表明，施P显著提高了4个密度大叶相思林土壤微生物的AWCD值、碳源利用丰富度指数、McIntosh指数、Shannon指数和Simpson指数，而施N和N+P则相反。随着林分密度的减小，各处理的土壤微生物AWCD值趋于减少。通常低密度林分的土壤微生物的丰富度指数、Shannon-Wiener指数、McIntosh指数和Simpson指数较小。;Climate change affects the physiological activities of soil microbes, which causes changes of soil microbial community structure and functional diversity and cascades the effects on biogeochemical cycling and climate-ecosystem feedbacks. Among them, nitrogen (N) and phosphorus (P) are considered as the limiting factors that influences the plant biodiversity and primary productivity in forest ecosystems. The external N addition or atmospheric N deposition has been found to affect the aboveground biology processes and the underground biochemistry of soil, both directly and indirectly. Chronic elevated N input has been shown to lead to many adverse impacts, including soil acidification, nutrients imbalance, and the increased greenhouse gas emissions. Forest soils of southern China are P-limited, because they are highly weathered and leached, and little P is released even from the weathering of primary P-bearing minerals. As a result, P fertilization is widely used in the subtropical forests of southern China. As an important component in regulating belowground ecological processes, the soil microbes are primary mediators of organic matter decomposition and nutrient cycling, and thus play a key role in maintaining function and sustainability of terrestrial ecosystems. Additionally, changes in soil microbial function and community composition may trigger a series of responses, such as impacting litter and organic matter decomposition rates, humus formation nutrient transformation and cycling, and then alter the interaction between soil microbes and plant communities. In this study, Biolog-ECO microplate method was used to investigate the interactive effects of nitrogen and phosphorus additions and different stand densities on soil microbial functional diversity of Acacia auriculiformis stands, which can provide a basis for establishing reasonable stand density, fertilization method, and improve soil quality. NH₄Cl and NaH₂PO₄·2H₂O were selected to simulate atmospheric nitrogen and phosphorus additions with 4 treatments (CK, N, P and N+P) and stand density was set at 4 levels (1667, 2500, 4444, and 10000 seedlings/hm²). The results showed that P treatment promoted the average well color development (AWCD) values, richness index, McIntosh index, Shannon index, and Simpson index of soil microbes in the four density stands, while the N and N+P treatments were opposite. With the decrease of forest density, the AWCD values of soil microbes in all treatments decreased. Generally, soil microbial richness index, Shannon-Wiener index, McIntosh index and Simpson index were small in the low density stands.

Effects of the Fertilizer Added with DMPP on Soil Nitrous Oxide Emissions and Microbial Functional Diversity

Agricultural sites contribute extensively to atmospheric emissions of climate-altering gases such as nitrous oxide. Several strategies have been considered to mitigate the impact of agriculture on climate, among these the utilization of fertilizers added with nitrification inhibitors such as DMPP (3,4-dimethylpyrazole phosphate) may represent a suitable solution. DMPP inhibits the growth and activity of ammonia-oxidizing microorganisms, particularly the ammonia-oxidizing bacteria, which are involved in N2O production. At present, little information is available on the effects of DMPP on the catabolic diversity of soil microbial community. In this study, the N2O emission by soil was performed by using the static chamber technique. The biological determinations of the microbial biomass carbon and the catabolic profile were assessed by measuring the substrate-induced respiration during the entire growing season of a potato crop under two nitrogen treatments: fertilization with and without DMPP. Our results did not show a clear mitigation of N2O emission by DMPP, even if a tendency to lower N2O fluxes in DMPP plots occurred when soil temperatures were lower than 20 °C. Conversely, DMPP deeply affected the microbial biomass and the catabolism of soil microorganisms, exerting a negative effect when it accumulated in excessive doses in the soil, limiting the growth and the capacity of soil microorganism communities to use different substrates.

Forest management practices of Pinus tabulaeformis plantations alter soil organic carbon stability by adjusting microbial characteristics on the Loess Plateau of China

Sustainable management practices can enhance the capacity and potential for soil carbon (C) sequestration, significantly contributing towards mitigating regional climate change. Here, we investigated how the microbial characteristics of a Pinus tabulaeformis plantation responded to different management practices to identify the role of microbial characteristics in influencing the stability of soil organic carbon (SOC). We chose a Pinus tabulaeformis plantation on the Loess Plateau where forest management practices had been conducted since 1999. Five forest management practices were implemented: two at the forest level (P. tabulaeformis with and without ground litter), and three using different vegetation restoration approaches after clear-cutting (P. tabulaeformis seedlings, abandoned grassland, and natural shrub regeneration). Microbial biomass, soil respiration, microbial community structure, microbial metabolic function, and soil oxidizable organic carbon (OC) fractions were evaluated. Forest management practices changed SOC stability by adjusting the microbial characteristics (e.g. soil microbial community diversity and microbial metabolic function diversity). The result of path analysis was that the direct path coefficient of microbial biomass on soil oxidizable OC fractions was the largest, which was 1.499. Path analysis and redundancy analysis showed that microbial biomass had the largest direct influence on soil oxidizable OC fractions. Compared with other forest management practices, natural shrub regeneration increased the nonlabile carbon fraction by increasing soil microbial characteristics, and contributed the most towards stabilizing SOC, which enhanced the stability of the soil ecosystem on the plateau. In conclusion, microbial biomass was the biggest influence factor of SOC stability. In contrast, the stability of SOC may be most stable in the area of natural shrub regeneration.

Soil microbial properties and functional diversity in response to sewage sludge amendments

ABSTRACT Soil organic matter has vital role in maintaining important soil functions. Consequently, using sewage sludge as soil organic amendment is considered one of the agricultural practices for improving soil fertility, which is also a safe approach for its disposal. The present research was carried out to analyze the different microbial activities and functional diversity of agricultural soil with regard to sewage sludge application. A laboratory experiment was set up by taking the agricultural soil from Haryana Agricultural University fields and amended with 5, 10, 20, 30 and 50 t ha−1 of sewage sludge. It was observed that soil microbial biomass increased upto 60% and potential activities of dehydrogenase, alkaline phosphatase and urease enzymes increased upto 50–55% with increasing application rates of sewage sludge. In addition the community-level physiological profiling technique (CLPP) based on carbon source utilization was used to determine the microbial functional diversity of soil. The results indicated higher functional diversity of microbial population capable of exploiting different carbon substrates with sewage sludge application. These results are imperative for improving the approach of sewage sludge application to the agricultural soil in consideration of increasing soil fertility with reducing the use of chemical fertilizers.

Contrasting rhizosphere bacterial communities of healthy and wilted Dalbergia sissoo Roxb. forests

The present study contrasted the bacterial communities of Dalbergia sissoo trees from forests with healthy trees, and forest with wilted trees. The bacterial diversity was assayed by Illumina MiSeq of the ribosomal hypervariable V3–V4 region. Metagenomic analysis revealed that microbial communities and functional diversity varied according to the plant health status. Presence of beneficial phyla such as Proteobacteria was observed lower in the soil of wilted trees than in those of healthy trees. The native microbial flora in wilted soil was highly suppressive and abundant in pathogenic bacterial genera such as Williamsia, Blastocatella, Methylobacterium, and Brevibacterium. The functional annotation of the data supports the cause of wilt in Pantnagar soil having an abundance of cellulolytic, xylanolytic, denitrifying bacteria, and the limitation of chitinolytic and nitrogen respiring bacterial population. This study paves the way for developing biological control strategies against wilted trees as well as a base for future identification and elucidation of bioinoculant microbes to secure the productivity of Dalbergia sustainably with changing weather and environmental conditions.

Soil Enzyme Activity and Microbial Metabolic Function Diversity in Soda Saline–Alkali Rice Paddy Fields of Northeast China

Western Jilin province has the most serious area of soda salinization in Northeast China, which affects and restricts the sustainable development of agriculture. The effects of physico-chemical properties of rhizosphere and non-rhizosphere soil on soil microbial diversity and enzyme activities (polyphenol oxidase, catalase, invertase, amylase) were evaluated in typical soda saline-alkali paddy field. Community-level physiological profile (CLPP) based on Biolog-ECO plates was used to assess the functional diversity of soil microorganisms. Exchangeable sodium percentage (ESP) and pH were negative correlated with the microbial activity (AWCD), soil enzyme activities (amylase, sucrose, and catalase, except for polyphenol oxidase) in rice rhizosphere and non-rhizosphere soil (P < 0.05). The indexes of microbial diversity in rice rhizosphere soil were significantly higher than that of non-rhizosphere soil. The utilization of amino acids by rice rhizosphere microorganisms was relatively high, while non-rhizosphere soil had relatively high utilization of carboxylic acid, phenolic acid, and amine. Among the selected physico-chemical properties, soil organic carbon (SOC) and soil water content (SWC) had the greatest influence on the variation of microbial diversity indexes and enzyme activities in rhizosphere soil. ESP and pH showed a significant positive correlation with carbon source utilization, especially for amine (AM) and phenolic acid (PA) carbon source utilization (P < 0.05) by means of RDA, and the utilization rate of AM and PA carbon sources by rice rhizosphere and non-root soil microorganisms was P1 < P2 < P3.

Characterization of Peat Microbial Functional Diversity in Aerobic Rice Rhizosphere

Microorganisms in the rhizosphere possess numerous metabolic activities. The addition of inorganic substance such as fertilizer could affect the microbial functional diversity. This study was conducted to evaluate the effect of different rate of NPK fertilizer on microbial functional diversity in the rhizosphere of local aerobic rice variety. Aerobic rice variety MRIA 1 was used in this study. Peat was taken from a non-agricultural area in Klang, Malaysia. The effect of fertilizer rate was determined with 4 different rates (C = non-fertilized; T1 = 100 kg/ha NPK; T2 = 200 kg/ha NPK; T3 = 400 kg/ha NPK). Microbial functional diversity was performed using Biolog™ Ecoplate System and measured by microbial activities, such as average well color development (AWCD), species richness (R), Shannon-Weaver index (H index) and species evenness (E). As a result, microbial activity increased to 5.7% when fertilizer applied at T2, while fertilizer rate at T3 increased species richness by 3.2%. However, addition of fertilizer did not affect the H index while species evenness slightly decreased by 1.1% when applied at T3. Bacteria population was reduced when fertilizer added at T1. Fertilizer addition to the peat soil decreased the culturable population of nitrogen-fixing microbes while no effect was found on culturable fungal, actinomycetes and phosphate-solubilizing microbe population. Microbes in T2 utilized many carbon sources. Variation in carbon sources used by microbes was found when fertilizer was applied at different rates. D-cellobiose, pyruvic acid methyl ester, and L-serine were the carbon sources that influenced the microbial function in soil. It is concluded that fertilizer has an effect on microbial functional diversity in the peat rhizosphere of local aerobic variety. The recommended fertilizer rate (T2) increased the microbial activity while high fertilizer rate (T3) increased species richness and decreased species evenness.

Effects of Chemical and Solar Soil-Disinfection Methods on Soil Bacterial Communities

The actctivated carbon + solar radiation membrane is an eco-friendly soil disinfestations method for managing soil-borne plant pathogens. However, little was known the impact of Activated carbon + solar radiation membrane on bacterial community structure in strawberry production systems under field conditions. A comprehensive evaluation of the impacts of different soil disinfection methods on the bacterial community structure is fundamental to understand the role of disinfection in maintaining soil health. The changes in the soil bacterial diversity and community composition were detected using realtime fluorescence quantitative PCR (RTFQ PCR) and next-generation sequencing techniques to better understand the effect of soil disinfection. The bacterial community composition was monitored after disinfection using dazomet (DZ), chloropicrin (CP), 100 kg/ha activated carbon + solar radiation membrane (AC1), 200 kg/ha activated carbon + solar radiation membrane (AC2), and 300 kg/ha activated carbon + solar radiation membrane (AC3) and compared with the control (CT). The results indicated that the different dosages of activated carbon (AC1, AC2, and AC3) did not affect the bacterial community structure. On the other hand, DZ and CP considerably reduced the soil biomass and abundance of bacterial species. Chemical fumigants influenced the bacterial community structure, with DZ treatment leading to the dominance of the phylum Firmicutes, accounting for approximately 54%. After fumigation with CP, Proteobacteria and Acidobacteria were the dominant phyla. Beta diversity analysis and principal coordinate analysis revealed that the bacterial communities in the soil treated with DZ and CP formed clusters. Redundancy analysis indicated that soil pH, available potassium, and available phosphorus were the key factors influencing microbial metabolic functional diversity. Thus, it was verified that the damage caused by activated carbon + solar radiation membrane—a potential alternative for chemical fumigant—to the soil bacterial community was less than that caused by chemicals DZ and CP.

Functional diversity of microbial communities in two contrasting maize rhizosphere soils

The characterization of microbial functional diversity proffers the opportunity to understand and manipulate them in various agricultural and biotechnological processes. This study analyzed the functional diversity and metabolic potentials of microbial communities in the rhizosphere of a former grassland and an intensively cultivated land using a shotgun metagenomic approach. We assumed that functional diversity will vary between the two maize fields and that each soil has an active metabolic profile that differentiates it from the other. Metagenomic DNA was extracted from the rhizosphere, and bulk soil samples from maize fields and sequencing was performed using the shotgun method. The results showed that 14 functional categories were dominant in the former grassland rhizosphere, while 12 functions predominated the intensively cultivated land. In the subsystems at level 2, potassium metabolism was the most abundant functional category with the highest relative abundance of 21.32% observed in GZ3. No significant difference was observed in the alpha diversity studies between the two fields, the Kruskal-Wallis test also revealed an insignificant difference (p = 0.99) in the diversity levels of samples, while 0.51 and 0.01 were obtained as the R- and p-values, respectively from the analysis of similarity (ANOSIM) performed. Nitrate nitrogen (N-NO3) was the most influential physicochemical parameter, with a p-value of 0.01 and a contribution % of 81.7%. Furthermore, the high abundance of unknown functions explains that the maize microbiome is still underexplored. Identifying the microbial communities with these functions will help in modeling them to harvest their unique functional benefits for agricultural productivity enhancement.

Afforestation suppresses soil nitrogen availability and soil multifunctionality on a subtropical grassland

Microbes simultaneously drive multiple functions (multifunctionality) that support human well-being. However, the structure and function of microbial communities and their impact on soil multifunctionality following grassland afforestation remains unknown, thus hindering our ability to formulate conservation policies. We compared soil bacterial and fungal communities, soil abiotic properties, and soil nitrogen (N) function and multifunctionality in the afforested sites that were previously grassland, on a subtropical plateau in China. We also explored the degree to which the niche complementarity effect and the selection effect of microbes are linked to soil N function and multifunctionality. We found that afforestation of grassland significantly decreased pH, available N concentration and density, and soil multifunctionality. However, afforestation significantly increased C (carbon) limitation and shifted soil microbes from being limited by N to, instead, being co-limited by N and P (phosphorus). The significant decrease in available N was primarily driven by soil microbes. In shaping soil N availability, the effect of bacterial diversities was stronger than that of fungal diversities, and the effect of fungal functional diversities was stronger than that of bacterial functional diversities. The effect of functional diversities was greater than that of all the significant changes in the functions and, also, the significant changes in the N-related functions. These results further emphasized that functional niche complementarity dominated soil N availability. In addition, bacterial taxonomic diversities showed positive effects of niche complementarity on soil multifunctionality; ultimately, the losses in bacterial taxonomic diversities derived from the increases in C limitation and the shifts in NP limitation combined to impaired soil multifunctionality. Our results suggested that the optimization of soil microbial functional diversities might increase soil N availability, and that minimizing losses of soil microbial taxonomic diversities by optimizing soil abiotic environments might improve soil multifunctionality.