Soil Microbial Community Function Research Articles

Microbial functional genes within soil aggregates drive organic carbon mineralization under contrasting tillage practices

AbstractSoil organic carbon (SOC) transformation is susceptible to tillage practices. Conservation tillage is known to optimize soil structure, improve microbial community diversity and increase SOC storage. However, how soil aggregate distribution and microbial community structure and function within aggregates affect SOC transformation under long‐term conservation tillage remains unclear. In this study, SOC mineralization dynamics were studied in situ and under laboratory conditions to examine the mechanisms by which C functional genes within soil aggregates of different sizes (i.e., mega‐, macro‐, and micro‐aggregates) influence SOC mineralization under long‐term tillage (i.e., zero, chisel, and plow tillage) in a dryland. The results indicated that in the winter wheat and summer maize rotation cropping system, SOC‐derived CO2‐C emissions were 143.99 and 133.29 g CO2‐C m−2 h−1 lower under chisel and zero tillage than that under plow tillage, respectively. Moreover, after 180 days of laboratory incubation, SOC mineralization in micro‐ and macro‐aggregates was 1.98 and 1.63 mg CO2‐C g−1 d−1 higher than that in mega‐aggregates, respectively. The aggregate‐associated differential modules of bacterial co‐occurring networks may be directly governed by bacterial community diversity and composition, which might play critical roles in driving SOC mineralization in response to different tillage intensities. Moreover, aggregate‐associated functional genes involved in labile and recalcitrant C compositions, which were determined by shotgun metagenomic sequencing, were associated with SOC mineralization and were significantly affected by the legacy effect of tillage intensity and aggregate size. Particularly, partial least squares path modeling revealed that genes involved in simple sugar metabolism exerted significantly positive effects on SOC mineralization, except for the effects of tillage intensity and aggregate size. Overall, this study showed that decreased abundances of labile C decomposition‐related functional genes within aggregates and community composition changes, as elucidated by the differences in bacterial network modules, under conservation tillage inhibit SOC mineralization. These findings may help in the development of adaptive soil tillage strategies for reducing carbon emissions in agroecosystems.

Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone.

Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.

The Effect of Human Trampling Activity on a Soil Microbial Community at the Urban Forest Park

Soil degradation resulting from human trampling in urban forest parks can negatively impact the taxonomic diversity and function of soil microbial communities. In this study, we established long-term, fixed large plots in Zijin Mountain Urban Forest Park in Nanjing, China, to assess the level of trampling pressure. Soil samples were collected from depths of 0–10 cm, 10–20 cm, and 20–30 cm for light trampling (LD), moderate trampling (MD), severe trampling (SD), extreme trampling (ED), and a no-trampling control (CK). The effects of different trampling pressures on soil were studied, including soil nutrient indices, microbial biomass, and the taxonomic diversity of fungi and bacteria. ANOVA and structural equation modeling (SEM) were employed to investigate the impacts of human trampling on the microbial community structure and function. The results indicated that soil organic carbon, ammonium, and acid phosphatase activity were the primary driving factors of microbial community change. Soil microbial diversity initially increased and then decreased with increasing trampling intensity. The changes in soil microbial function and classification were found to be associated with the intensity of trampling. Moderate trampling could enhance the diversity of the soil microbial community. The succession pattern of the fungi and bacteria communities was distinct, and the composition of the bacteria community remained relatively stable. Trampling impacts vegetation and soil structure, which then affects the structure and function of the microbial community. This study provides an essential foundation for the restoration of compacted soil in urban forest parks through targeted monitoring and management efforts.

Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion.

Plant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood. Here, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies. As a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils. Our study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.

Seasonal variations of soil bacterial and fungal communities in a subtropical Eucalyptus plantation and their responses to throughfall reduction.

Climatic change causes obvious seasonal meteorological drought in southern China, yet there is a lack of comprehensive in situ studies on the effects of drought in Eucalyptus plantations. Here, a 50% throughfall reduction (TR) experiment was conducted to investigate the seasonal variations of soil bacterial and fungal communities and functions in a subtropical Eucalyptus plantation and their responses to TR treatment. Soil samples were collected from control (CK) and TR plots in the dry and rainy seasons and were subjected to high-throughput sequencing analysis. Results showed that TR treatment significantly reduced soil water content (SWC) in the rainy season. In CK and TR treatments, fungal alpha-diversity decreased in the rainy season while bacterial alpha-diversity did not change significantly between dry and rainy seasons. Moreover, bacterial networks were more affected by seasonal variations compared with fungal networks. Redundancy analysis showed that alkali hydrolyzed nitrogen and SWC contributed the most to the bacterial and fungal communities, respectively. Functional prediction indicated that the expression of soil bacterial metabolic functions and symbiotic fungi decreased in the rainy season. In conclusion, seasonal variations have a stronger effect on soil microbial community composition, diversity, and function compared with TR treatment. These findings could be used to develop management practices for subtropical Eucalyptus plantations and help maintain soil microbial diversity to sustain long-term ecosystem function and services in response to future changes in precipitation patterns.

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.

New insights into the effects of antibiotics and copper on microbial community diversity and carbon source utilization.

Residual antibiotics (ABs) and heavy metals (HMs) are continuously released from soil, reflecting their intensive use and contamination of water and soil, posing an environmental problem of great concern. Relatively few studies exist of the functional diversity of soil microorganisms under the combined action of ABs and HMs. To address this deficiency, BIOLOG ECO microplates and the Integrated Biological Responses version 2 (IBRv2) method were used to comprehensively explore the effects of single and combined actions of copper (Cu) and enrofloxacin (ENR), oxytetracycline (OTC), and sulfadimidine (SM2) on the soil microbial community. The results showed that the high concentration (0.80mmol/kg) compound group had a significant effect on average well color development (AWCD) and OTC showed a dose-response relationship. The results of IBRv2 analysis showed that the single treatment group of ENR or SM2 had a significant effect on soil microbial communities, and the IBRv2 of E1 was 5.432. Microbes under ENR, SM2, and Cu stress had more types of available carbon sources, and all treatment groups were significantly more enriched with microorganisms having D-mannitol and L-asparagine as carbon sources. This study confirms that the combined effects of ABs and HMs can inhibit or promote the function of soil microbial communities. In addition, this paper will provide new insights into IBRv2 as an effective method to evaluate the impacts of contaminants on soil health.

Associations of soil bacterial diversity and function with plant diversity in Carex tussock wetland.

Some species of Carex can form tussocks, which are usually distributed in valleys and flood plains. The soil microbial community diversity and function of micro-habitats formed by tussocks are associated with plant diversity, and research on these associations can guide Carex tussock wetland restoration. In this study, we selected tussock wetlands dominated by Carex appendiculata, including natural wetlands (NW), artificially restored wetlands (ARW), and naturally restored wetlands (NRW), and investigated plant diversity. Soil samples were collected from the quadrats of each sample plot with the maximum (ma), median (me), and minimum (mi) plant Shannon index values, and high-throughput sequencing was used to analyze the bacterial community composition, diversity, and functions. The plant diversity indexes of neither ARW nor NRW significantly differed from that of NW, but the companion species in NRW were hygrophytes and mesophytes, in contrast to only hygrophytes serving as companion species in NW and ARW. The soil bacterial communities at the operational taxonomic unit level of the nine quadrats with different plant Shannon index values significantly (p < 0.01) differed. The relative abundances of the dominant phyla (Proteobacteria, Chloroflexi, and Bacteroidetes) and the dominant genera (Geobacter, Sideroxydans, and Clostridium except for unassigned genera) significantly (p < 0.05) differed under the different levels of plant diversity. The plant Shannon index, soil moisture content, total organic carbon, N, and P were significantly (p < 0.05 or p < 0.01) correlated with the bacterial Shannon index. The phylogenetic diversity of the bacterial community in NW was significantly (p < 0.0001) different from those in ARW and NRW, and that in ARW was also significantly (p < 0.05) different from that in NRW. The functional groups of bacterial communities associated with plant diversity. In the NWme, ARWme, and NRWme bacterial communities, the relative proportions of functional groups related to soil N cycle were higher, but those related to soil S and C cycles were lower. Considering the rehabilitation of both plant and microbial communities, the methods used for establishing the ARW are recommended for Carex tussock wetland restoration.

Microbial Community Structure and Predictive Functional Analysis in Reclaimed Soil with Different Vegetation Types: The Example of the Xiaoyi Mine Waste Dump in Shanxi

We explored the characteristics of soil bacterial communities and their ecological functions under different types of vegetation reclamation in open-pit mines on the Loess Plateau, which is the guiding significance for the selection of vegetation and the improvement of restoration effect in mining areas. The research object was to reclaim the soil of the aluminum mine waste dump in Xiaoyi County, Shanxi. The soil characteristics were measured under different types of vegetation reclamation. The soil bacterial community under different vegetation reclamation was measured using the 16S rRNA gene high-throughput sequencing technology. The ecological function was predicted using the PICRUSt method. The correlation between soil physical and chemical properties and bacterial community structure and function was analyzed. From the results, (1) the bacterial compositions of the reclaimed soil samples were 33 phyla, 90 classes, 121 orders, 207 families, 298 genera, and 140 species. The abundance and diversity of the soil microbial community showed the rule of yellow rose &gt; lespedeza and sweet wormwood herb &gt; alfalfa. (2) Proteobacteria were the dominant bacteria in alfalfa and sweet wormwood herb samples, accounting for 36.09–43.36%. Proteobacteria and actinobacteria were the dominant bacteria in the yellow rose and lespedeza samples accounted for 53.34–53.39%. α-Proteobacteria, actinobacteria, and β-proteobacteria were the dominant bacteria of the four vegetation types. The relative abundance of the α-proteobacteria and β-proteobacteria was positively correlated with soil organic carbon (SOC) and negatively correlated with soil total kalium (TK). Actinobacteria were positively correlated with available kalium (AK) and negatively correlated with SOC and total nitrogen (TN). (3) There was no difference in the primary functions of the soil bacterial community after the reclamation of different plants, and the main functions were metabolism, genetic information processing, and environmental information processing, with the function abundance accounting for 81.52%. (4) The abundance of functional genes in the metabolism of other amino acids, folding, sorting, and degradation and glycan biosynthesis and metabolism were relatively rich in the rhizosphere soil of yellow rose. The abundance of functional genes in signal molecules and interaction, transport, and catabolism in the rhizosphere soil of lespedeza was the highest. The abundance of functional genes in carbohydrate metabolism, translation, and energy metabolism in the rhizosphere soil of alfalfa was the highest. Therefore, there were significant differences in the structure and function of rhizosphere soil microbial communities among yellow rose, lespedeza, sweet wormwood herb, and alfalfa, and they were also affected by the soil properties. Hence, we concluded that the differences and diversity of soil microbial structure and function can help select plants for the sustainable development of soil remediation in mining areas.

Revealing the Effect of Saline Water Drip Irrigation on Soil Microorganisms in Cotton Fields Based on Metagenomics

Saline water irrigation has become an important means to alleviate the shortage of freshwater in arid areas. However, long-term saline water irrigation can cause soil salinity accumulation, affect soil microbial community structure, and then affect soil nutrient transformation. In this study, we used metagenomics to investigate the effects of long-term saline water drip irrigation on soil microbial community structure in a cotton field. In the experiment, the salinity of irrigation water (ECw) was set to two treatments:0.35 dS·m-1 and 8.04 dS·m-1 (denoted as FW and SW, respectively), and the nitrogen application rates were 0 kg·hm-2and 360 kg·hm-2 (denoted as N0 and N360, respectively). The results showed that saline water irrigation increased soil water content, salinity, organic carbon, and total nitrogen content and decreased soil pH and available potassium content. Nitrogen fertilizer application increased soil organic carbon, salinity, and total nitrogen content and decreased soil water content, pH, and available potassium content. The dominant bacterial phyla in each treatment were:Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Gemmatimonadetes. Saline water irrigation significantly increased the relative abundances of Actinobacteria, Chloroflexi, Gemmatimonadetes, and Firmicutes but significantly decreased the relative abundances of Proteobacteria, Acidobacteria, Cyanobacteria, and Nitrospira. Nitrogen fertilizer application significantly increased the relative abundances of Chloroflexi and Nitrospira but significantly decreased the relative abundances of Acidobacteria, Gemmatimonadetes, Planctomycetes, Cyanobacteria, and Verrucomicrobia. LEfSe analysis showed that saline water irrigation had no significant effect on the number of potential biomarkers, and nitrogen fertilizer application decreased the number of potential biomarkers in soil microbial communities. The correlation network diagram showed that the 20 genera had different degrees of correlation, including 44 positive correlations and 48 negative correlations. The core species in the network diagram were Nocardioides, Streptomyces, Pyrinomonas, Candidatus_Solibacter, and Bradyrhizobium spp. Saline water irrigation increased the relative abundances of the denitrification genes nirK, nirS, nasB, and norC and decreased the relative abundances of the nitrification genes amoB, amoC, and nxrA, whereas nitrogen fertilizer application increased the relative abundances of the nitrification genes amoA, amoB, amoC, hao, and nxrA and decreased the relative abundances of the denitrifying genes narB, napA, nasA, and nosZ. Saline water irrigation could adversely affect soil physicochemical properties; SWC, EC1:5, and BD were the main driving factors affecting soil microbial community structure and function genes; and soil microorganisms adapted to soil salt stress by regulating species composition.

Soil variables driven by host plant and growth season affect soil microbial composition and metabolism in extremely arid desert ecosystems

Assessment changes of soil microbial community structure and function is important in understanding the response to desert ecosystem management. In present study, variations of soil microbial community and edaphic factors associated with five desert shrubs were determined in Anxi extremely arid desert in Northwest China in growing (summer), deciduous (autumn), and snowfall (winter) seasons. For that, the microbial composition and catabolic metabolism were examined using methods of phospholipid fatty acid (PLFA) and Biolog EcoPlate, respectively. Regardless of plant species and seasonal patterns, the microbial community was mostly dominated by gram-negative bacteria (GN); and the carbohydrates, amino acids and polymers were the main carbon sources for desert microbial metabolism. Microbial biomass and metabolic levels were significantly higher in both summer and winter than those of autumn. There was no correlation between soil microbial community and carbon utilization in winter; but GN was positively correlated with metabolism of amines carbon sources in summer, while fungal community presented the strongest correlation with suites of carbon sources’ metabolic levels in autumn, indicating the uncoupled relationship between microbial community and function in desert ecosystems. Desert shrubs significantly influenced the composition of soil microbial community, whereas the variation of microbial catabolic metabolism was most attributed to seasonality. Nevertheless, the effects of both plant species (21.3 %) and climate variation (84.9 %) interacted with soil properties, indicating the seasonality of soil nutrients predominately determined the changes in composition and metabolism of desert microbes. Both the comprehensive seasonal level and the intra-seasonal paired correlation analysis proved that phosphorus was the key factor in determining microbial community composition, while ammonia and nitrate nitrogen were more correlated to microbial functional metabolism. Additionally, soil moisture and organic carbon in desert environment also induced the shifts in ratio of fungi and bacterial communities. We conclude that the seasonal patterns of soil microbial community and metabolic function in extremely arid desert are predictable, and mainly influenced by specific soil factors driven by desert shrubs and climate factors. These findings will provide a basis for evaluating the management of soil resources and microbial function in desert environments.

The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research.

Continuous cultivation of ginseng crops in fixed plots can lead to disease outbreaks, yield losses and replanting failures. Fallow periods can help restore soil health and increase the sustainability of agricultural systems; however, taking land out of production for extended periods is often not feasible. Short-term fallow periods could restore soil health, but few studies have examined the effects of short-term fallow treatment on the health of soil in ginseng fields. In this preliminary study, we used metagenomic analysis to assess changes in the abundance of major ginseng pathogens and soil health overall following a short-term fallow period in a region in the Changbai Mountains. A sample from a forest plot (Hx0ks), was compared to a sample from a field where ginseng was previously cultivated and then had been left fallow for two years (Hx2), and a sample from a field that had been fallow for two years and was subsequently replanted with ginseng (Clsd). Soil that was fallow for two years, and then replanted with ginseng, showed reduced nutrient content and lower diversity of soil bacterial and fungal communities than soil that remained fallow. Candidatus Solibacter (5%) and Rhizomicrobium (3%) were the most abudant bacterial genera in Hx2. Rhizomicrobium (4%) and Gemmatimonas (3%) were the most abundant bacterial genera in Clsd. Mortierella (22%) and Peziza (12%) dominated the fungal community in Hx2. Lecanicillium (38%) and Mortierella (13%) dominated the fungal community in Clsd. Fallow periods also increased the functional diversity of soil as predicted by PICRUSt and decreased the relative abundance of the pathogenic fungi. Preliminary findings were consistent with the hypothesis that fallow management in ginseng cultivation can improve soil microbial community structure and function and reduces the number of plant pathogens; however, testing this hypothesis will require replicated plots.

Structure and Function Analysis of Cultivated Meconopsis integrifolia Soil Microbial Community Based on High-Throughput Sequencing and Culturability

(1) Background: The structure, function, and community interactions of soil microbial communities of cultivated Meconopsis integrifolia were characterized by studying this alpine flower and traditional endangered Tibetan medicine. (2) Methods: Soil bacteria and fungi were studied based on high-throughput sequencing technology. Bacteria were isolated using culturomics and functionally identified as IAA-producing, organic phosphorus-dissolving, inorganic phosphorus-dissolving, and iron-producing carriers. (3) Results: The dominant bacterial phyla were found to be Proteobacteria and Acidobacteria, and unclassified_Rhizobiales was the most abundant genus. Ascomycota and Mortierellomycota were the dominant fungal phyla. The bacteria were mainly carbon and nitrogen metabolizers, and the fungi were predominantly Saprotroph-Symbiotroph. The identified network was completely dominated by positive correlations, but the fungi were more complex than the bacteria, and the bacterial keystones were unclassified_Caulobacteraceae and Pedobacter. Most of the keystones of fungi belonged to the phyla Ascomycetes and Basidiomycota. The highest number of different species of culturable bacteria belonged to the genus Streptomyces, with three strains producing IAA, 12 strains solubilizing organic phosphorus, one strain solubilizing inorganic phosphorus, and nine strains producing iron carriers. (4) Conclusions: At the cost of reduced ecological stability, microbial communities increase cooperation toward promoting overall metabolic efficiency and enabling their survival in the extreme environment of the Tibetan Plateau. These pioneering results have value for the protection of endangered Meconopsis integrifolia under global warming and the sustainable utilization of its medicinal value.

Application of microbial organic fertilizers promotes the utilization of nutrients and restoration of microbial community structure and function in rhizosphere soils after dazomet fumigation.

Soil fumigant dazomet is a broad-spectrum nematicide and fungicide that can kill non-target microbes. Fungicides or organic fertilizers are often added after fumigation to improve the recovery of soil microbes. However, the effect of adding microbial organic fertilizers (MOF) after fumigation on the structure and function of rhizosphere soil microbial communities of crops is unclear. Therefore, we investigated the effects of adding Junweinong and Junlisu MOFs after dazomet fumigation on the structure and function of rhizosphere microbial communities and its relationship with soil properties and enzyme activities. The results showed that the addition of these two MOFs after dazomet fumigation significantly reduced the rhizosphere soil available phosphorus, available potassium, organic matter content, and urease, alkaline phosphatase, and catalase activities, but increased the soil pH compared with the fumigation treatment. The application of MOFs after fumigation resulted in significant enrichment of bacteria such as Gaiella, norank_f_Vicinamibacteraceae, and Flavisolibacter and fungi such as Peroneutypa, Olpidium, and Microascus in the rhizosphere soil of the crop and increased the relative abundance of functional genes of 13 kinds of amino acids metabolism, pyruvate metabolism, TCA cycle, and pentose phosphate pathway as well as endophytic and epiphytic functional groups in the rhizosphere soil. In particular, NH4 +-N, pH, and AK had the greatest effect on rhizosphere microorganisms. Overall, the addition of MOFs after fumigation promoted crop root nutrient uptake, enhanced rhizosphere soil microbial metabolism, allowed more beneficial communities to colonize the roots, and promoted soil microbiological health.

Unique Habitat of Karst Tiankengs Changes the Taxonomy and Potential Metabolism of Soil Microbial Communities.

Microbial communities in karst ecosystems have been extensively studied. However, in a class of deep-lying habitats with unique climates (karst tiankeng), the structure and ecological functions of microorganisms receive little attention, which is essential for understanding the biogeochemistry of karst tiankeng. Herein, microorganisms from inside (ITK) and outside (OTK) karst tiankengs were analyzed by high-throughput sequencing and multivariate statistical analysis. The results showed that the structure and function of soil bacterial communities inside and outside karst tiankengs were significantly different. The ITK microbial communities presented significantly higher Shannon diversity due to the abundant nutrients in karst tiankeng soil. Random molecular ecological network analysis revealed that the ITK network was simpler and more vulnerable and may be susceptible to environmental changes. More positive links within the network indicate that microorganisms adapt to the karst tiankeng through synergies. The keystones in karst tiankeng were mainly involved in the decomposition of soil organic matter and carbon/nitrogen cycles. Although soil total phosphorus and available potassium regulate microbial community structure variation, dispersal limitation is the predominant ecological process within the microbial community in karst tiankeng. In addition, the functional profiles of the microbial communities reveal that some human diseases (such as infectious diseases) exist in OTK. Collectively, these findings have enhanced our understanding of microbial interactions, ecological functions, and community composition processes in karst tiankeng ecosystems. IMPORTANCE Constrained by the trapped terrain, a unique ecosystem has formed in karst tiankeng. Soil microorganisms are essential for the formation and maintenance of ecosystems, but soil microbial ecology research in karst tiankeng is still lacking. In this study, representative habitats inside and outside karst tiankeng were selected to study the taxonomy and potential metabolism of soil microbial communities. The results show that the unique habitat of karst tiankeng reshapes the composition, structure, and function of soil microbial communities. Our results contribute to enhancing our understanding of sustainable recovery strategies in fragile ecosystems and understanding the biodiversity value of karst tiankeng under climate change.

Effects of solarisation combined with compost on soil pathogens and the microbial community in a spinach cropping system

This study compares the effects of solarization combined with compost (72% vineyard prunings and 28% leek residues) (CAS) versus solarization (NAS) in soils used for intensive spinach cultivation in the Mediterranean area. The objective was to study the beneficial effects of the compost on the soil microbial community, soil fertility and soil functionality related to C and N cycling during solarization, during the spinach crop growth period and after harvesting. CAS did increase soil fertility and microbial activity, in addition, CAS increased the microbial alpha diversity in the soil to a greater extent than NAS, and the Principal Coordinate Analysis (PCoA) of the beta diversity in the soil revealed changes in the bacterial and fungal community at the different sampling times, except after the plastic was lifted. During solarization and after harvesting, different beneficial bacteria and fungi related to C and N cycling were more abundant in CAS than in NAS, in the same way as the genera involved in plant defense and plant growth (Pseudomonas, Sphingomonas, Bacillus, Thermomyces, Streptomyces, NMD1 or Nitrospira). CAS also had a notable effect on the abundance of predictive genes involved in the C and N cycles. The functional genes showed their lowest activity level a week after covering the soil with plastic, but they increased after lifting the plastic and after harvesting. Compared to NAS, CAS also showed higher N2-fixation and greater conversion of N2O to N2. Moreover, the abundance of several predictive genes involved in hemicellulose, lignin and cellulose degradation suggested that CAS produced an increase in nutritional availability. From this study, it can be concluded that the combination of solarization and compost increased soil fertility, microbial activity, microbial diversity and functionality. Compost could provide added value by stimulating the microbiological community in the soil until harvest.

The Effects of Atrazine, Diuron, Fluazifop-P-butyl, Haloxyfop-P-methyl, and Pendimethalin on Soil Microbial Activity and Diversity

Understanding the impacts of herbicides on soil microbial communities is important, as these organisms mediate a wide range of ecosystem services. Here, we investigated whether the diversity and function of soil microbial communities were significantly influenced by one-off applications of atrazine, diuron, fluazifop-P-butyl, haloxyfop-P-methyl and pendimethalin as pure compounds at their recommended doses over multiple time points (1, 3, 7, 14, 30 and 60 days). Phylogenetic marker gene sequencing revealed that none of the herbicides influenced the numbers of bacterial and archaeal taxa or the evenness of their abundances. Similarly, none of the herbicides influenced the composition of bacterial and archaeal communities, except for diuron, fluazifop-P-methyl and pendimethalin, which were associated with larger relative abundances of a small number of OTUs on day 30 only. Functionally, none of the herbicides significantly influenced fluorescein diacetate hydrolysis (FDA) and beta-glucosidase activities or the induced respiratory responses of soil microbial communities to a range of substrates. These data indicate that the active herbicide ingredients tested may have minimal non-target effects when applied once at their recommended dose. Given their frequent use, it is important to next consider whether these herbicides have more pronounced effects at higher doses and application frequencies.

Effects of Continuous Straw Returning on Soil Functional Microorganisms and Microbial Communities

This study examined the changes in soil enzymatic activity, microbial carbon source metabolic diversity, and straw decomposition rates in paddy fields treated with 1, 2, or 3years of straw returning (SR1-SR3). The soil's ability to decompose straw and cellulolytic bacteria increased with the number of treatment years (1: 31.9% vs. 2: 43.9% vs. 3: 51.9%, P < 0.05). The numbers of Azotobacter, Nitrobacteria, cellulolytic bacteria, and inorganic phosphate bacteria increased progressively with the numbers of straw returning years. Cellulolytic bacteria and inorganic phosphate bacteria were significantly positively correlated with the decomposition rate (r = 0.783 and r = 0.375, P < 0.05). Based on 16S sequencing results, straw returning improved the microbial diversity of paddy soils by increasing unclassified bacteria and keeping dominant soil microorganism populations unchanged. The relative importance of individual microbial taxa was compared using random forest models. Proteobacteria, ammoniating bacteria, and potassium dissolving bacteria contributed to peroxidase activity. The significant contributors to phosphate monoesterase were Acidobacteriota, Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria. Proteobacteria, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to urease activity. Desulfobacterota, ammoniating bacteria, cellulolytic bacteria, and potassium-dissolving bacteria contributed to the neutral invertase activity. In conclusion, soil microbial community structure and function were affected within 2years of straw returning, which was driven by the combined effects of soil organic carbon, available nitrogen, available potassium, and pH. With elapsing straw returning years, soil properties interacted with soil microbial communities, and a healthier soil micro-ecological environment would form.

An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria

BackgroundGastrodia elata Bl. f. glauca, a perennial herb of G.elata Bl. in Orchidaceae, is one of the most valuable traditional Chinese medicines. G. elata Bl. is a chlorophyll-free myco-heterotrophic plant, which must rely on the symbiotic growth of Armillaria, but not all Armillaria strains can play the symbiotic role. Additionally, Armillaria is easy to degenerate after multiple generations, and the compatibility between the strains from other areas and G. elata Bl. f. glauca in Changbai Mountain is unstable. Therefore, it is incredibly significant to isolate, identify and screen the symbiotic Armillaria suitable for the growth of G. elata Bl. f. glauca in Changbai Mountain, and to explore the mechanism by which Armillaria improves the production performance of G. elata Bl. f. glauca.ResultsFirstly, G. elata Bl. f. glauca tubers, and rhizomorphs and fruiting bodies of Armillaria were used for the isolation and identification of Armillaria. Five Armillaria isolates were obtained in our laboratory and named: JMG, JMA, JMB, JMC and JMD. Secondly, Armillaria was selected based on the yield and the effective component content of G. elata Bl. f. glauca. It was concluded that the yield and quality of G. elata Bl. f. glauca co-planted with JMG is the highest. Finally, the mechanism of its high quality and yield was explored by investigating the effects of different Armillaria strains on the soil, its nutrition element contents and the soil microbial diversity around G. elata Bl. f. glauca in Changbai Mountain.ConclusionsCompared with commercial strains, JMG significantly increased the content of Na, Al, Si, Mn, Fe, Zn, Rb and the absorption of C, Na, Mg, Ca, Cr, Cu, Zn and Rb in G. elata Bl. f. glauca; it improved the composition, diversity and metabolic functions of soil microbial communities around G. elata Bl. f. glauca at phylum, class and genus levels; it markedly increased the relative abundance of bacteria such as Chthoniobacter and Armillaria in the dominant populations, and enhanced such functions as Cell motility, amino acid metabolism and Lipid metabolism; it dramatically decreased the relative abundance of Bryobacter and other fungi in the dominant populations, and reduced such functions as microbial energy metabolism, translation and carbohydrate metabolism. This is the main reason why excellent Armillaria strains promote the high quality and yield of G. elata Bl. f. glauca in Changbai Mountain.

Comparison of soil microbial community structure and function for karst tiankeng with different degrees of degradation.

Karst tiankengs are oases in degraded karst landscapes and act as repositories for biodiversity conservation; however, knowledge about the bacterial and fungal structure and function of the karst tiankeng ecosystems is limited. This study investigated the microbial communities in three different tiankeng (nondegraded, moderately degraded, and heavily degraded tiankeng) by Illumina NovaSeq sequencing. We found that the degradation of karst tiankeng can lead to changes in microbial community structure and functions, while there are differences in bacterial and fungal responses. There were significant differences in bacterial and fungal community composition and beta diversity in the three tiankeng soils. Random molecular ecological network analysis results indicated that a more complex and stable bacterial network existed in nondegraded tiankeng, while more complex fungal networks existed in moderately degraded tiankeng. The keystones of Proteobacteria, Actinobacteria, Acidobacteria, Ascomycota, and Basidiomycota played essential roles in maintaining soil function and stability. The functional profiles revealed that tiankeng habitat changes may affect microbial survival strategies, such as increasing gene abundance associated with the carbon cycle. To our knowledge, this is the first report on bacterial and fungal communities in different degrees of karst tiankeng, which provides crucial insights into our understanding of the microbial communities' structure and potential function in karst tiankeng ecosystems.