Soil Microbial Community Structure Research Articles

No tillage and organic fertilization improved kiwifruit productivity through shifting soil properties and microbiome

AbstractThe preservation of edaphic quality and productivity is critical for the ecological sustainability of vine orchards. The heavy utilization of intensified tillage and singular chemical fertilizers can shift changes in edaphic physicochemical and biological features, thus exerting significant pressure on agroecosystems. In current research, we assessed the shifts in soil physicochemical features and soil microbiome composition over 11 years carrying out no tillage and organic fertilizer substitution in a typical Chinese Guanzhong kiwifruit production area, and explore the fundamental factors that contribute to alterations in the microbial community and the influence on kiwifruit performance. Results showed that long‐term no tillage and organic fertilizer improved the soil condition by significantly increasing the proportion of soil macroaggregates, bulk density, and nutrient content (e.g., organic matter, nitrogen, and ammonia), as compared to conventional tillage with chemical fertilization. Moreover, no tillage significantly increased soil bacterial α‐diversity but had no significant effects on fungal. No tillage also enhanced the abundance of potential beneficial soil bacteria (e.g., Acidobacteria, Actinobacteria, and Nitrospira), while decreasing the abundance of Proteobacteria, Pseudomonas, and Fusarium. In addition, no tillage and mixed fertilized soil microbial network exhibited higher complexity (i.e., node and edge numbers, and positive edge proportion) and connectivity (i.e., average number of neighbors) than conventional tillage and chemical fertilization group. Changes in nitrate, ammonia, available phosphorus, and pH values accounted for the variation in the structure of soil microbial community. Hence, the utilization of both no tillage and organic fertilization practices could serve as a suitable and sustainable approach for managing kiwifruit production in the fragile environmental conditions of the Chinese Guanzhong region, and lead to an improvement in soil nutrient levels and help regulate the soil microbial community.

Organic substitution regime with optimized irrigation improves potato water and nitrogen use efficiency by regulating soil chemical properties rather than microflora structure

Context or problemImproving water and fertilizer use efficiency is an inevitable choice for sustainable potato production in North China. However, the regulation mechanism of potato water and nitrogen use efficiency under water-nitrogen coupling (W-N) regime is still unknown. Objective or research questionThe objectives from a 3-year field experiment were (1) to assess the impact of W-N regimes on potato yield and water and nitrogen use efficiency, (2) to elucidate the soil microflora structure under W-N regimes, and (3) to determine the relationship between soil chemical properties, microflora structure, and potato water and nitrogen use efficiency. MethodsA three-year two-factor split-zone potato field experiment was conducted in arid and semi-arid regions of the Inner Mongolian Plateau, with irrigation [(rainfed (W0), optimized (soil-based) irrigation (W1), conventional irrigation (W2)] as the primary treatment and N fertilizer [no N (N0), chemical N (N1), 25 % manure substitution (N2)] as the secondary treatment. ResultsPotato yield and water productivity followed N2 > N1 > N0, and partial nitrogen productivity and nitrogen agronomic efficiency followed N2 > N1 at the same irrigation level. Potato yield, nitrogen internal efficiency, partial nitrogen productivity and nitrogen agronomic efficiency first increased and then decreased, whereas water productivity gradually decreased with increasing irrigation levels under the same fertilization regime. Moreover, potato yield, soil total nitrogen, organic carbon, and microbial biomass carbon and nitrogen content peaked with the W1N2 regime. W-N regimes significantly influenced soil microbial community structure. Soil microbial α-diversity was less variable under W1 and N2 conditions. Soil bacterial network complexity and robustness were higher in W1 and W2 than in W0 regimes, whereas the opposite was true for fungi. The complexity and robustness of the soil bacterial and fungal network demonstrated for three fertilization regimes were higher in N1 and N2 than in N0 regimes. Neutral community model showed that soil microflora in W-N regime was mainly influenced by stochastic processes. PLSPM showed that organic substitution regime with optimized irrigation improves potato water and nitrogen use efficiency by regulating soil chemical properties rather than microflora structure. ConclusionsW1N2 regime synergizes well to improve potato water and N use efficiency and soil microflora stability, and organic substitution regime with optimized irrigation improves potato water and nitrogen use efficiency by regulating soil chemical properties. Implications or significanceOur findings initially clarified the regulatory mechanisms of potato water and nitrogen use efficiency in North China, offering theoretical guidance for further optimizing irrigation and fertilization management.

Nonbiodegradable microplastic types determine the diversity and structure of soil microbial communities: A meta-analysis

As an emerging contaminant, microplastics (MPs) have received considerable attention for their potential threat to the soil environment. However, the response of soil bacterial and fungal communities to MPs exposure remains unclear. In this study, we conducted a global meta-analysis of 95 publications and 2317 observations to assess the effects of nonbiodegradable MP properties and exposure conditions on soil microbial biomass, alpha and beta diversity, and community structure. Our results indicate that MPs increased (p < 0.05) soil active microbial biomass by 42%, with the effect varying with MPs type, exposure concentration, exposure time and soil pH. MPs concentration was identified as the most important factor controlling the response of soil microbial biomass to MPs. MPs addition decreased (p < 0.05) the soil bacterial Shannon and Chao1 indices by 2% and 3%, respectively, but had limited effects (p > 0.05) on soil fungal Shannon and Chao1 indices. The type of MPs and exposure time determined the effects of MPs on bacterial Shannon and Chao1 indices, while the type of MPs and soil pH controlled the response ratios of fungal Shannon and Chao1 indices to MPs. Specifically, soil organic carbon (SOC) was the major factor regulating the response ratio of bacterial alpha diversity index to MPs. The presence of MPs did not affect soil bacterial community structure and beta diversity. Our results highlight that MPs reduced bacterial diversity and richness but increased the soil active microbial biomass, suggesting that MPs could disrupt biogeochemical cycles by promoting the growth of specific microorganisms.

Changes in soil bacterial community diversity and its network stability under different grazing intensities in plateau rangelands

Grassland degradation is a significant ecological challenge, it changes the grassland environment, including the structure of soil microbial communities. Grazing is a critical factor in this process, yet the impact of different grazing intensities on soil bacterial communities, particularly in unique environments like the Qinghai-Tibet Plateau, remains poorly understood. This study utilized a full-length 16 S rRNA gene sequencing technology combined with environmental factors to assess the impacts of the Holba sheep grazing on soil bacterial community diversity in Zhongba County, Shigatse City, Qinghai-Tibet Plateau. The specific aim was to explore the changes in soil bacterial community diversity and stability under contrasting grazing intensities: prohibited grazing, light grazing, moderate grazing, and heavy grazing. The results showed that grazing activities significantly altered the diversity of bacterial communities, particularly under light and heavy grazing. The spatial dissimilarity in soil bacterial communities was mainly driven by species turnover (i.e., species replacement), which was more pronounced under heavy grazing. The number of keystone species increased with the grazing intensity of the bacterial co-occurrence network. Under heavy grazing, bacterial communities showed the highest number of keystone species and the community stability. Environmental factors such as exchangeable magnesium (EM), soil available kalium (SAK), and soil pH were the most important environmental variables impacting changes in bacterial community structure by influencing community α-diversity and stability. This study enhances our understanding of the response mechanisms of soil microbial communities to grazing intensities and other environmental stresses in grassland ecosystems. In addition, this study also provides important references and guidance for microbial diversity research in extreme environments. These findings are crucial for promoting the sustainable management and conservation of grassland ecosystems in climatically harsh areas such as the Qinghai-Tibet Plateau.

Soil Microbial Community Structure and Carbon Stocks Following Fertilization with Organic Fertilizers and Biological Inputs.

The application of organic fertilizers and biological inputs to soil inevitably affects its quality, agrochemical indicators, and microbiota. Sustainable agriculture is based on continuously learning about how to properly manage available soil, water, and biological resources. The aim of the study was to determine changes in microorganism communities and carbon stocks in infertile soils for fertilization using different organic fertilizers and their combinations with bio-inputs. Genetic analysis of microorganism populations was performed using the NGS approach. Our study showed that the application of organic fertilizers affects the soil microbiota and the taxonomic structure of its communities. Specific groups of bacteria, such as Bacillota, were promoted by organic fertilization, meanwhile the abundance of Pseudomonadota and Ascomycota decreased in most treatments after the application of poultry manure. Metagenomic analysis confirmed that the use of bio-inputs increased the relative abundance of Trichoderma spp. fungi; meanwhile, a significant change was not found in the representatives of Azotobacter compared to the treatments where the bio-inputs were not used. The positive influence of fertilization appeared on all the studied agrochemical indicators. Higher concentrations of Corg and Nmin accumulated in the soil when we used granulated poultry manure, and pHKCl when we used cattle manure.

Soil Microbial Community Structures under Annual and Perennial Crops Treated with Different Nitrogen Fertilization Rates

Perennial bioenergy crops may enhance microbial community structures due to their extensive root system compared to annual crops. However, the long-term effect of perennial bioenergy crops receiving different N fertilization rates on microbial community structures is not well defined. We evaluated the 11-year effect of perennial bioenergy crops with various N fertilization rates as well as an annual crop with the recommended N rate on soil microbial properties in 2019 and 2020 in the US northern Great Plains. Perennial grasses were intermediate wheatgrass, IWG (Thinopyrum intermedium [Host] Barkworth and Dewey), and switchgrass, SG (Panicum virgatum L.), with N fertilization rates of 0, 28, 56, and 84 kg N ha−1, and the annual crop was spring wheat, WH (Triticum aestivum, L.) with 80 kg N ha−1. The total fungal phospholipid fatty acid (PLFA) proportion and fungal/bacterial ratio were significantly lower under annual spring wheat than perennial grass (SG). Increased N fertilization rate linearly increased Gram-positive bacterial PLFA proportions and the Gram-positive/Gram-negative bacterial ratio for IWG in 2020 but decreased the PLFA proportions of arbuscular mycorrhizal fungi (AMF) for both perennial bioenergy crops in all years. The proportions of AMF neutral lipid fatty acid and Gram-negative bacterial PLFA were greater for SG (0.432 and 0.271, respectively) than IWG (0.339 and 0.258, respectively), but actinomycetes and the Gram-positive/Gram-negative bacterial ratio were greater for IWG (0.160 and 1.532, respectively) compared to SG (0.152 and 1.437, respectively). Microbial community structures varied with perennial bioenergy crops, N fertilization rates, and perennial vs. annual crops. This study showed how perennial crops favored fungal growth and how annual crops enhanced bacterial growth impacting soil biological health.

Nitrogen-fixing bacteria promote growth and bioactive components accumulation of Astragalus mongholicus by regulating plant metabolism and rhizosphere microbiota

BackgroundThe excessive application of chemical fertilizers in the cultivation of Astragalus mongholicus Bunge results in a reduction in the quality of the medicinal plant and compromises the sustainable productivity of the soil. PGPB inoculant is a hot topic in ecological agriculture research. In the cultivation of Astragalus mongholicus, the screened nitrogen-fixing bacteria can promote plant growth, however, whether it can promote the accumulation of main bioactive components remains unknown. In this study, mixed inoculants containing 5 strains of growth promoting bacteria (Rhizobium T16, Sinorhizobium T21, Bacillus J1, Bacillus G4 and Arthrobacter J2) were used in the field experiment. The metabolic substances in the root tissues of Astragalus mongholicus were identified during the harvest period by non-targeted metabolomics method, and the differential metabolites between groups were identified by statistical analysis. Meanwhile, high-throughput sequencing was performed to analyze the changes of rhizosphere soil and endophytic microbial community structure after mixed microbial treatment.ResultsThe results of non-targeted metabolism indicated a significant increase in the levels of 26 metabolites after treatment including 13 flavonoids, 3 saponins and 10 other components. The contents of three plant hormones (abscisic acid, salicylic acid and spermidine) also increased after treatment, which presumed to play an important role in regulating plant growth and metabolism. Studies on endosphere and rhizosphere bacterial communities showed that Rhzobiaceae, Micromonosporaceae, and Hypomicrobiaceae in endophytic, and Oxalobactereae in rhizosphere were significantly increased after treatment. These findings suggest their potential importance in plant growth promotion and secondary metabolism regulation.ConclusionsThis finding provides a basis for developing nitrogen-fixing bacteria fertilizer and improving the ecological planting efficiency of Astragalus mongholicus.

Impact of alternate partial root-zone irrigation on the rhizosphere microbiota of alfalfa plants inoculated with rhizobia.

Water is an important constraint on alfalfa (Medicago sativa) production in arid and semiarid areas, and alternate irrigation in root areas has water-saving potential for alfalfa production. To investigate the impact of alternate partial root-zone irrigation (APRI) on the rhizosphere soil microorganisms of alfalfa, this study subjected alfalfa plants to different irrigation methods and irrigation levels. The growth status and rhizosphere soil microbial community diversity of alfalfa plants under alternate root-zone watering treatment were analyzed through laboratory experiments and high-throughput sequencing. The results showed that at soil moisture levels of 80% field moisture capacity (FMC) and 60% FMC, APRI had no significant impact on the biomass or nodule number of alfalfa. However, 40% FMC significantly reduced the individual plant dry weight, chlorophyll content, and nodule number of the alfalfa plants. APRI increased the relative abundance of Actinomycetes in the alfalfa rhizosphere soil. Moreover, at 60% FMC, the MBC and MBN of rhizosphere, relative abundance of Actinobacteria and unclassified K fungi and Chao 1 index of bacteria significantly increased under APRI treatment. While relative abundance of Ascomycetes and Proteobacteria in the alfalfa rhizosphere significantly reduced under 60% FMC + APRI treatment. In summary, under the same irrigation conditions, APRI did not significantly affect the growth of alfalfa in the short term. And 60%FMC + APRI treatment did significantly affect the groups, structure and diversity of the rhizosphere soil microbial communities.

Exotic plants introduction changed soil nutrient cycle and symbiotic relationship with arbuscular mycorrhizal fungi in wetland ecological projects.

In the process of applying exotic plants to wetland ecological restoration, insufficiently evaluated alien species may exhibit strong competitiveness and fecundity. Once introduced, they can displace native flora, disrupt the original ecological balance, diminish biodiversity, and even induce ecosystem dysfunction. Furthermore, exotic plants have the potential to alter soil microbial community structure, including the composition and activity of beneficial symbiotic microorganisms such as arbuscular mycorrhizal fungi (AMF), thereby impacting soil nutrient cycling and interplant nutrient competition. Here, we conducted three consecutive years of sampling experiments to investigate the succession of AMF communities associated with the invasive plant Spartina alterniflora along an initial introduction chronosequence, and to identify the key environmental factors influencing its response to S. alterniflora invasion. Our findings reveal that early-stage invasion by S. alterniflora alters the composition of soil AMF communities with unclassified_c__Glomeromycetes and Glomus-viscosum-VTX00063 consistently dominating. Additionally, as the duration of introduction increases, the diversity of rhizosphere soil AMF significantly decreases, while its evenness remains relatively stable. It's indicated that soil ω, AN, AK and N/P ratio were the main influencing factors of the integral AMF community. Notably, soil available phosphorus (AP) emerges as a positive influence on the important AMF taxa. The results confirm the mutual feedback effect between the invasion of the perennial herb S. alterniflora and AMF, in which specific AMF assist in nutrient absorption to promote S. alterniflora growth, potentially facilitating its rapid and successful invasion of new habitats. Given the likely differential effects of AMF communities on various plant species, our findings could contribute to anticipating future AMF-mediated effects during the introduction of alien plants.

Unveiling soil microbial community dynamics in desertification: A case study from the tianshan mountains, xinjiang

Microorganisms constitute the primary ecological group in desertified soil, driving soil biogeochemical cycles. Understanding their structure and diversity is crucial for the ecological restoration of desertification areas. This study focuses on the typical desert slopes in the eastern section of the northern foothills of the Tianshan Mountain in Xinjiang, China. It investigates changes in the main prokaryotic microbial community structure, including bacteria and archaea, and their relationship with environmental factors. Results show generally low soil water content, increasing with depth, and a weak alkaline nature with no significant vertical variations. While microbial communities do not distinctly respond to soil water content, there are noticeable variations in microbial diversity with clear stratification, negatively correlated with total organic carbon. Molecular ecological network analyses of five bare soil profiles in Xinjiang’s Hami Tianshan Desert reveal positive interactions among soil microorganisms in vertical layers. Surprisingly, the topsoil, despite having complex networks, shows low diversity and weak interconnectivity. Intriguingly, subsurface soils exhibit distinct molecular ecological networks similar to those found in ecological transition zones (These zones are characterized by rapid environmental shifts from one type to another), further highlighting significant ecological disparities between surface and subsurface soils. By analyzing the structure of soil microbial communities and their relationship with environmental factors on typical desert slopes in the Tianshan Mountains of Xinjiang, significant microbial ecological differences are found between surface and subsurface soils. Notably, in subsurface soils, microbial networks similar to those in ecological transition zones are discovered. These areas have complex microbial community structures and diverse ecological functions, providing new insights into the mechanisms of ecological restoration in desertified soils. Consequently, this study suggests that the vertical distribution patterns of microbial communities in bare desert soil areas differ from those in vegetated areas such as forests and grasslands. The interactions among species, the unique distribution of soil organic matter, and various physical factors are likely pivotal in the distribution patterns of microbial communities in bare desert soils. This research provides foundational theories and empirical support for the ecological restoration of bare desert soils.

Differences in Soil Fertility and Bacterial Community Structure Between Carbon Inputs such as Biochar and Organic Fertilizer and Their Relationship

The potato planting area of Guizhou Province ranks second in China. However, due to factors such as climatic conditions and unbalanced fertilization, soil organic matter in potato fields is consumed rapidly and has a large deficit, which affects soil biological function and soil fertility. Biochar and organic fertilizer are effective ways to supplement foreign aid organic matter to improve soil quality. However, the differences in soil fertility and microbial community structure and their relationships under the conditions of organic fertilizer or biochar combined with chemical fertilizer are not clear. In this study, three treatments of conventional fertilization （NPK）, increased application of biochar （NPKB）, and increased application of organic fertilizer （NPKO） were set up to investigate the characteristics of potato rhizosphere soil, bacterial community composition, and diversity； to analyze the effects of these factors on the soil integrated fertility index； and to explore the direct and indirect effects of IFI on soil fertility and bacterial community structure differences between treatments and their driving factors. The results showed that soil pH, available phosphorus （AP）, available potassium （AK）, total nitrogen （TN）, organic carbon （SOC）, and C/N ratio were significantly higher in the NPKB and NPKO treatments than in the NPK treatment （P<0.05）. Soil IFI was greatest for NPKO, followed by NPKB and least for the NPK treatment. A total of 8 214 ASVs were obtained from all the soil samples, belonging to 26 phyla, 75 classes, 165 orders, 176 families, and 251 genera （excluding unidentified fungi）. Proteobacteria, Actinobacteria, and Chloroflexi were the dominant phyla, accounting for 54.85% of all ASVs. Compared to that in the NPK and NPKB treatments, the NPKO treatment had the highest bacterial diversity and number of significantly different taxa, and soil AN, AP, AK, SOC, TN, and IFI were significant correlates of bacterial diversity index （P<0.05）. Additionally, pH, TN, and SOC were significant influencers of bacterial taxa differences （P<0.05）, with importance ranked as TN （70.59%） &gt; SOC （49.42%） &gt; pH （27.08%）. Structural equations suggested that pH-related soil properties and bacterial community diversity were the direct pathways influencing IFI, and soil pH-related soil characteristics could also indirectly affect IFI by affecting bacterial Shannon diversity. These results indicate that soil fertility and bacterial community structure were significantly different and correlated between the biochar and organic fertilizer addition treatments and that pH and bacterial community diversity were the key factors influencing IFI, with the NPKO treatment in particular having the best effect on improving IFI. Considering the effect of soil fertilization and the functional group of bacteria, NPKO is the recommended combination for the best synergistic effect of soil fertilization, that is, N 150 kg·hm-2+P2O5 135 kg·hm-2+K2O 135 kg·hm-2+organic fertilizer 6.6 t·hm-2.

Long-term nitrogen deposition alters the soil bacterial community structure but has little effect on fungal communities

Subtropical Moso bamboo (Phyllostachys edulis) forests have become hot spots for nitrogen (N) deposition in China. However, the effect of long-term N deposition on the structure of soil microbial communities in different horizons of these forests remains unclear. To investigate the influence of extended N deposition on soil bacteria and fungi, a simulated N deposition field study was conducted in Fujian Province with four N deposition levels (0, 20, 40 and 80 kg N hm−2 a−1). The absolute abundances, diversity, community structure, and potential functions of soil bacteria and fungi were investigated after 10 years of simulated N deposition. The results indicated that there was no significant effect of N deposition on the abundance or diversity of soil microbes in either the organic or mineral horizons of Moso bamboo forests. However, under rates of 40 and 80 kg N hm−2 a−1, long-term N deposition altered the structure of the soil bacterial community in the organic horizon. Specifically, there was a 27.75∼36.40 % increase in the relative abundance of Actinobacteria, while that of Acidobacteria decreased by 24.40∼27.52 %. Redundancy analysis (RDA) demonstrated that soil total carbon (TC) was the key variable influencing the bacterial community structure in the organic horizon. Analysis of potential microbial functions showed that in the organic horizon, the rates of chemoheterotrophy significantly decreased under 80 kg N hm−2 a−1. However, N deposition did not noticeably impact the fungal community structure in either soil horizon. Our study suggested that under 10 years of N deposition, only the bacterial community composition and function in the organic horizon was affected, indicating that soil bacteria are more sensitive to N deposition than fungi in subtropical Moso bamboo forests. Therefore, further research is necessary to fully understand the impact of N deposition on fungal community composition in the soil organic horizon and on the microbial community in the mineral horizon of subtropical bamboo forests. This study provides valuable insights for informing future environmental management and conservation strategies.

New insights into assembly processes and driving factors of urban soil microbial community under environmental stress in Beijing

Rapid urbanization leads to drastic environmental changes, directly or indirectly affecting the structure and function of soil microbial communities. However, the ecological response of soil microbes to environmental stresses has not yet been fully explored. In this study, we used high-throughput sequencing to analyze the assembly mechanism and driving factors of soil microbial community under environmental stresses. The results indicated that environmental stresses significantly affected soil properties and the levels of beryllium, cobalt, antimony, and vanadium contamination in soil generally increased from the suburban areas toward the city core. The composition and distribution of soil microbial communities demonstrated clear differences under different levels of environmental stress, but there was no significant difference in microbial diversity. Random forest and partial least squares structural equation modeling results suggested that multiple factors influenced microbial diversity, but antimony was the key driver. The influence of environmental stress led to deterministic processes dominating microbial community assembly processes, which promoted the regional homogenization of soil microbes. Therefore, this study provides new insights into urban soil microbial management under environmental stresses.

Response of soil microbial diversity and functionality to snow removal in a cool-temperate forest

Climate-induced changes in thinning snowpack can greatly impact soil freeze-thaw patterns and water supply. These effects may influence the soil microbial diversity and the key ecological functions mediated by microorganisms, thereby altering the cycling of nutrient in the ecosystem. A snow-exclusion experiment to explore the effects of snow removal on soil microbial diversity and functionality in Larix gmelinii forest. Control (natural snowfall), SR (complete snow removal) and SR-SR (complete snow removal, with snow returned for water supplementation at the end of winter) were represented three experimental treatments. The results showed that: snow removal resulted in more severe soil frost in winter. Soil nitrogen availability was higher in the snow removal plots compared to control plots in freeze-thaw period. Fungal diversity was not affected by snow removal, neither the α diversity of bacteria. However, snow removal did alter the bacterial community structure. These changes of the above did not persist into the growing season. SR-SR significantly reduced soil multifunctionality during freeze-thaw period, whereas SR did not. However, SR and SR-SR resulted in significantly higher soil multifunctionality than was observed in control during early growing season. Additionally, a widespread increase in the abundance of nitrogen cycling genes was observed in the SR and SR-SR plots during the freeze-thaw period and the early growing season, respectively. Snow removal significantly affected soil multifunctionality, which can be explained by changes in the microbial biomass, bacterial community structure and network complexity. Furthermore, snow removal significantly altered soil water content, temperature, and dissolved carbon, nitrogen. dbRDA and random forest analysis showed that soil water content, temperature, and total nitrogen as drivers of soil microbial community structure and multifunctionality. This study highlights that snow removal altered soil nitrogen availability, microbial community diversity, and multifunctionality during freeze-thaw period. However, these changes did not result in cross-seasonal legacy effects.

Response of soil microbial community structure and function to the sewage leakage: A case study of a 25-year-old cesspool

Providing many millions of rural households with decentralized sanitation facilities remains challenging. In undeveloped areas, cesspools have still been widely used due to technologically simple and low-cost. However, the influence of cesspools on the surrounding soil remains unclear. In this study, we investigated the influence of a 25-year-old household cesspool on soil physicochemical factors, microbial community composition and function, pathogens and antibiotic resistance genes (ARGs). Soil at the depth around the sewage liquid level (D70) was mostly disturbed where TOC, NO3–N and TP was increased to 16.8 g/kg, 18.2 mg/kg and 1.02 mg/kg respectively. Correspondingly, the element cycling genes of carbon fixation, methanotrophy, nitrogen fixation, ammonia oxidation, and nitrate reduction etc., were increased at D70. Notably, human derived pathogens such as Enterobacter, Salmonella, Pseudomonas aeruginosa, Klebsiella pneumoniae, Prevotella, and Vibrio were highly enriched by 5–10 folders in D70, indicating the potential health risk to human. Mantel tests suggested that EC, TP, pH, NH3–N and particularly NO3–N are important factors that influence the microbial community and element cycling genes in cesspool-affected soil. Overall, this study revealed the impact of household cesspool leakage on the surrounding soil and provided information for the selection and construction of basic sanitation facilities in poor regions.

Comparative Metagenomic Analysis Reveals Rhizosphere Microbiome Assembly and Functional Adaptation Changes Caused by Clubroot Disease in Chinese Cabbage.

Clubroot is a major disease and severe threat to Chinese cabbage, and it is caused by the pathogen Plasmodiophora brassicae Woron. This pathogen is an obligate biotrophic protist and can persist in soil in the form of resting spores for more than 18 years, which can easily be transmitted through a number of agents, resulting in significant economic losses to global Chinese cabbage production. Rhizosphere microbiomes play fundamental roles in the occurrence and development of plant diseases. The changes in the rhizosphere microorganisms could reveal the severity of plant diseases and provide the basis for their control. Here, we studied the rhizosphere microbiota after clubroot disease infections with different severities by employing metagenomic sequencing, with the aim of exploring the relationships between plant health, rhizosphere microbial communities, and soil environments; then, we identified potential biomarker microbes of clubroot disease. The results showed that clubroot disease severity significantly affected the microbial community composition and structure of the rhizosphere soil, and microbial functions were also dramatically influenced by it. Four different microbes that had great potential in the biocontrol of clubroot disease were identified from the obtained results; they were the genera Pseudomonas, Gemmatimonas, Sphingomonas, and Nocardioides. Soil pH, organic matter contents, total nitrogen, and cation exchange capacity were the major environmental factors modulating plant microbiome assembly. In addition, microbial environmental information processing was extremely strengthened when the plant was subjected to pathogen invasion, but weakened when the disease became serious. In particular, oxidative phosphorylation and glycerol-1-phosphatase might have critical functions in enhancing Chinese cabbage's resistance to clubroot disease. This work revealed the interactions and potential mechanisms among Chinese cabbage, soil environmental factors, clubroot disease, and microbial community structure and functions, which may provide a novel foundation for further studies using microbiological or metabolic methods to develop disease-resistant cultivation technologies.

Insight into interaction among soil microbial community, soil metabolomics and enzyme activity after long-term PAH stress

The problem of soil polycyclic aromatic hydrocarbon (PAH) pollution in coking plant sites has been widely studied in recent years, but there is a lack of research on the correlation between soil microorganisms, soil metabolomics, and soil properties. Thus, in this study, the long-term impact of coke combustion on soil microbial community structure, enzyme activities, and metabolic pathways within a former coking plant site was investigated. Soil samples were collected from both the coking production area (CA group) and office area (OLA group), approximately 0 to 20 cm in depth. Compared with OLA group, elevated levels of 16 PAHs in the list of USA EPA were detected by gas chromatography-mass spectrometry in the CA group. Several dominant microorganisms, such as Altererythrobacter, Lysobacter, and Sulfurifustis, were identified by 16 s ribosomal DNA sequencing in the CA group. The fatty acid biosynthesis pathway exhibited specific inhibition, while the phenylalanine metabolic pathway was promoted in response to PAH stress. Long-term PAH exposure led to the inhibition of soil urease activity. The co-occurrence network of microorganisms revealed intricate patterns of co-metabolism and co-adaptation within complex bacterial communities, facilitating their adaptation to and decomposition of soil-borne PAHs. This research could provide valuable insights into the community characteristics and metabolic mechanisms of microorganisms inhabiting PAH-polluted soil within coking plant sites. The findings enhance our understanding of the indigenous soil microbiome and its intricate network dynamics under the persistent stress of PAHs, contributing to a more comprehensive knowledge of soil ecosystems in such environments.

Soil Microbial Community Structure and Its Contribution to Carbon Cycling in the Yalu River Estuary Wetland

Wetland microbial communities play a vital role in ecosystem functioning, particularly in the intricate processes of carbon cycling. This study employed metagenomic sequencing to investigate the diversity, composition, structural differences, carbon cycling functional gene, and microbial species of soil microbial communities in five distinct soil types of the Yalu River estuary wetland, including shoal soil, bog soil, paddy soil, meadow soil, and brown forest soil. We further explored the influence of environmental factors on both the microbial community structure and carbon cycling functional genes. Our results revealed a bacterial-dominated soil microbial community, constituting about 97.6%. Archaea and fungi represented relatively minor fractions, at 1.9% and 0.4%, respectively. While no significant differences were observed in Chao1 indices between bacterial and fungal communities, the Shannon index revealed notable differences. Both Chao1 and Shannon indices exhibited significant variations within the archaeal communities. The dominant bacterial phyla were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae. Thaumarchaeota, Crenarchaeota, and Euryarchaeota formed the major archaeal phyla, while Ascomycota, Mucoromycota, and Basidiomycota were the dominant fungal phyla. Non-metric multidimensional scaling (NMDS) analysis based on Bray-Curtis distance revealed notable differences in the bacterial, archaeal, and fungal community structures across the samples. Redundancy analysis (RDA) identified key environmental factors for the major phyla. Soil pH, soil organic carbon (SOC), electrical conductivity (EC), and total phosphorus (TP) were the main influencing factors for bacteria, while soil TP, EC, total sulfur (TS), and SOC were the primary drivers for archaeal phyla. Soil total nitrogen (TN) and EC were the main influencing factors for fungal phyla. Analysis of key carbon cycling pathway genes utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and clustering heatmap revealed some variations in functional gene composition across different soil types. Mantel test indicated that pH, TN, and SOC were the primary environmental factors influencing microbial functional genes associated with soil carbon cycling. Stratified bar chart analysis further demonstrated that the major contributors to carbon cycling originated from corresponding dominatnt phyla and genera of Proteobacteria, Thaumarchaeota, Actinomycetota, Euryarchaeota, and Bacteroidota. The species and relative abundance of microorganisms associated with carbon cycling pathways varied among the samples. These findings provide a crucial reference for informing the conservation and sustainable management of wetland ecosystems in the Yalu River estuary.

A review of factors affecting the soil microbial community structure in wetlands.

Microbial community in wetland soils is crucial for maintaining the stability of the wetland ecosystem. Nevertheless, the soil microbial community is sensitive to the environmental stress in wetlands. This leads to the possibility that the microbial community structure may be influenced by environmental factors. To gain an in-depth understanding in the response of microbial community structure in wetland soils under different environmental factors, this review comprehensively explores the factors of natural conditions (e.g., different types of wetland, soil physical and chemical properties, climate conditions), biological factors (e.g., plants, soil animals), and human activities (e.g., land use, soil pollution, grazing). Those factors can affect microbial community structure and activities in wetland soils through different ways such as (i) affecting the wetland soil environment in which soil microorganisms survived in, (ii) influencing the available nutrients (e.g., carbon, nitrogen) required for microbial activity, and (iii) the direct effects on soil microorganisms (toxicity or promotion of resistant species). This review can provide references for the conservation of microbial diversity in wetland soils, the maintenance of wetland ecosystem balance, and the wetland ecological restoration.

Performance and mechanistic study of biochar and magnesium-enhanced phytoremediation in cadmium-contaminated soil by alfalfa

Recently, phytoremediation has been regarded as a green and environment friendly technique to treat metals contaminated soils. Thus, in this study, pot experiments were designed to investigate the combine effects of biochar and magnesium (MPs) to purify cadmium (Cd)-contaminated soils by Medicago sativa L. (alfalfa). The results showed that the combined use of biochar and Mg significantly increased the accumulation of Cd and promoted the transport of Cd from root to shoot in alfalfa, simultaneously. Importantly, the combined use of biochar and Mg could increase the accumulation of Cd in shoot and whole plant (shoot + root) of alfalfa up-to 59.1% and 23.1%, respectively. Moreover, the enhancement mechanism can be analyzed from several aspects. Firstly, the photosynthesis was enhanced, which was beneficial to plant growth. The product of photosynthesis provided energy for uptake and transport of Cd. Meanwhile, its transport in phloem could promote the transport of Cd. Secondly, the enhancement of antioxidant capacity of alfalfa effectively protected the membrane structure of alfalfa, which indicated that Cd could enter alfalfa from the channel on the cell membrane. Lastly, the chemical form of Cd and microbial community structure in soil were changed. Overall, these changes reduced the Cd toxicity in soil, enhanced the resistance capability of alfalfa, increased the Cd uptake by alfalfa and promoted the growth of alfalfa. Thus, the obtained results suggested that the combined use of biochar and Mg is an effective approach to enhance phytoremediation performance for purifying Cd-contaminated soils.