Diversity Of Soil Microorganisms Research Articles

Seasonality and vegetation shape the taxonomic and functional diversity of microorganisms in islands of fertility of a semi-arid region in the Colombian tropics

The islands of fertility or resource islands play a crucial role in combating desertification, as they harbor diverse microbial communities essential for their establishment. The objective of this study was to determine the taxonomic and functional diversity of soil microorganisms in a semi-arid region of the Colombian tropics using a metagenomic approach. To achieve this, we sampled three species of nurse trees as well as bare soil during both the dry and wet seasons. Total DNA was extracted and sequenced extensively. Taxonomic diversity was established by comparing against the SILVA database, while functional diversity was determined using the DIAMOND program and the KEGG database. The analysis unveiled seasonal microbial dynamics influenced by vegetation cover. Islands of fertility exhibited higher diversity and nutritional value compared to bare soil. Wet season conditions boosted microbial diversity, narrowing the gap between vegetated and unvegetated soils. Under drought conditions, Proteobacteria predominated in the resource islands, while Actinobacteria prevailed in the bare soil. Both islands of fertility and the rainy season are significant drivers of microbial communities in these semi-arid environments. The presence of unique genera indicated specialized adaptations, revealing an under-explored microbial diversity. Although complete methanogenesis was absent, methane oxidation pathways were detected. Bacteria demonstrated notable adaptations for nitrate reduction, even under organic substrate limitation. Organic matter and anaerobic microenvironments could play a crucial role in nitrate reduction and denitrification. Sulfate reduction prevailed during the dry season, whereas thiosulfate oxidation was more prominent during the wet season. These findings underscore the remarkable adaptability of microbial communities in challenging environments and provide key insights for addressing desertification in semi-arid zones.

Understanding and exploring the diversity of soil microorganisms in tea (Camellia sinensis) gardens: toward sustainable tea production.

Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes' function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production.

Soil Geobacteraceae are the key predictors of neurotoxic methylmercury bioaccumulation in rice.

Contamination of rice by the potent neurotoxin methylmercury (MeHg) originates from microbe-mediated Hg methylation in soils. However, the high diversity of Hg methylating microorganisms in soils hinders the prediction of MeHg formation and challenges the mitigation of MeHg bioaccumulation via regulating soil microbiomes. Here we explored the roles of various cropland microbial communities in MeHg formation in the potentials leading to MeHg accumulation in rice and reveal that Geobacteraceae are the key predictors of MeHg bioaccumulation in paddy soil systems. We characterized Hg methylating microorganisms from 67 cropland ecosystems across 3,600 latitudinal kilometres. The simulations of a rice-paddy biogeochemical model show that MeHg accumulation in rice is 1.3-1.7-fold more sensitive to changes in the relative abundance of Geobacteraceae compared to Hg input, which is recognized as the primary parameter in controlling MeHg exposure. These findings open up a window to predict MeHg formation and accumulation in human food webs, enabling more efficient mitigation of risks to human health through regulations of key soil microbiomes.

Multiple nutrient limitation of the soil micro-food web in a tropical grassland revealed by nutrient-omission fertilization

Although involved in key functions of the terrestrial ecosystems, the activity and the diversity of soil microorganisms can be severely limited by energy and nutrients in weathered tropical soils. To optimize nutrient cycling for crop nutrition, assessing which nutrients limit the activity of the microbial food web is thus essential. This was our aim in this study carried out on a tropical ferrallitic soil from a natural grassland in Madagascar. For this purpose, we employed an innovative nutrient-omission approach in microcosms to test the distinct effects of omitting C, six nutrients (N, P, K, S, Ca, Mg) and a cocktail of micronutrients (B, Mn, Cu, Na and Mo) on the composition, biomass and activities of the microbial community and on the abundance and biomass of their nematode grazers. C and P were identified as primary limitations, but other nutrients (N, Mg and S) played significant roles as co-limiting factors. Some bacterial and fungal taxa were significantly associated to specific nutrient deficiencies and can act as biological indicators. Additionally, the abundance and biomass of microbial-feeding nematodes provided valuable insights into the responses of the soil microbial community to nutrient deficiencies. These findings contribute to our understanding of nutrient dynamics and microbial community growth in tropical grassland ecosystems and have implications for sustainable crop fertility management and ecosystem ecology in similar environments.

Tourmaline-enhanced bioremediation of Cd/BDE-153 co-contaminated soil: Migration, soil microorganism structure and enzyme activities

The efficient remediation of the soil co-contaminated with heavy metals and polybrominated diphenyl ethers (PBDEs) from electronic disassembly zones is a new challenge. Here, we screened a fungus of F. solani (F.s) can immobilize Cd and remove PBDEs. wIt combined with tourmaline enhances the remediation of co- pollutants in the soil. Furthermore, the environment risks of the enhanced technology were assessed through the amount of Cd/BDE-153 in Amaranthus tricolor L. (amaranth) migrated from soil, as well as the changes of soil microorganism communities and enzyme activities. The results showed the combined treatment of tourmaline and F.s made the removal percentage of BDE-153 in rhizosphere soil co-contaminated with BDE-153 and Cd reached 46.5%. And the weak acid extractable Cd in rhizosphere soil decreased by 33.7% compared to control group. In addition, the combined remediation technology resulted in a 32.5% (22.8%), 45.5% (37.2%), and 50.7% (38.1%) decrease in BDE-153 (Cd) content in the roots, stems, and leaves of amaranth, respectively. Tourmaline combined with F.s can significantly increase soil microorganism diversity, soil dehydrogenase and urease activities, further improving the remediation rate of Cd and BDE-153co-pollutants in soil and the biomass of amaranth. This study provides the remediation technology of soil co-contaminated with heavy metal and PBDEs and ensure the maintenance of food security.

Identification of bacteria and fungi responsible for litter decomposition in desert steppes via combined DNA stable isotope probing.

Soil microorganisms play crucial roles in determining the fate of litter in desert steppes because their activities constitute a major component of the global carbon (C) cycle. Human activities lead to increased ecosystem nitrogen (N) deposition, which has unpredictable impacts on soil microorganism diversity and functions. Nowadays, it is necessary to further study the succession of these microorganisms in the process of litter decomposition in desert steppe, and explore the effect of N deposition on this process. This issue is particularly important to resolve because it contributes to the broader understanding of nutrient cycling processes in desert steppes. In this study, DNA stable isotope probing (DNA-SIP) was used to study changes in soil bacterial and fungal community composition and function during 8 weeks of culture of 13C-labeled litter in desert steppes. The results were as follows: (1) Actinomycetota, Pseudomonadota, and Ascomycota are the main microorganisms involved in litter decomposition in desert steppes; (2) N deposition (50 kg ha-1 year-1) significantly increased the relative abundance of some microorganisms involved in the decomposition process; and (3) N deposition likely promotes litter decomposition in desert steppes by increasing the abundances of N cycles bacteria (usually carrying GH family functional genes). These findings contribute to a deeper understanding of the C assimilation mechanisms associated with litter residue production, emphasizing the importance of extensive C utilization.

Metagenomics study of soil microorganisms involved in the carbon cycle in a saline-alkaline meadow steppe in the Songnen Plain in Northeast China.

Soil microorganisms play an important role in regulating and contributing to carbon cycling processes in grassland ecosystems. Soil salinization is one of the major problems causing soil degradation, and its effects on carbon cycle immobilization-related functional genes in soil microorganisms remain unknown. Therefore, we took Songnen salinization grassland as the research object, selected grasslands with different salinization levels, and explored the diversity of soil microorganisms and functional genes related to carbon cycling in Songnen grassland with different salinization levels through metagenomic technology. The results showed that with the increase of salinity, the relative abundance of Ascomycetes increased, while the relative abundance of Proteus and Firmicutes decreased. In addition, the relative abundance of functional genes related to carbon cycling fixation has also decreased. As the degree of soil salinization increases, the relative abundance of glycoside hydrolases (GH)130 family significantly increases, while the relative abundance of soil carbohydrate enzymes belonging to GH3 and GH55 families significantly decreases. Using structural equation modeling (SEM), it was found that soil pH and conductivity (EC) have a significant impact on soil microbial diversity and functional genes related to carbon cycling fixation. The increase in soil pH directly reduces the Shannon diversity of soil microbial diversity and functional genes related to carbon cycling fixation. Therefore, it can be concluded that the intensification of grassland salinization reduces the diversity of bacteria and fungi, and affects the diversity of functional genes related to carbon cycling fixation by reducing the total diversity of bacteria. The increase in salinity has a negative feedback effect on grassland soil carbon cycling. This study provides a theoretical framework for grassland soil carbon sequestration and degradation restoration.

Responses of plant diversity and soil microorganism diversity to nitrogen addition in the desert steppe, China

Nitrogen (N) deposition is a significant aspect of global change and poses a threat to terrestrial biodiversity. The impact of plant-soil microbe relationships to N deposition has recently attracted considerable attention. Soil microorganisms have been proven to provide nutrients for specific plant growth, especially in nutrient-poor desert steppe ecosystems. However, the effects of N deposition on plant soil microbial community interactions in such ecosystems remain poorly understood. To investigate these effects, we conducted a 6-year N-addition field experiment in a Stipa breviflora Griseb. desert steppe in Inner Mongolia Autonomous Region, northern China. Four N treatment levels (N0, N30, N50, and N100, corresponding to 0, 30, 50, and 100 kg N/(hm2•a), respectively) were applied to simulate atmospheric N deposition. The results showed that N deposition did not significantly affect the aboveground biomass of desert steppe plants. N deposition did not significantly reduce the alfa-diversity of plant and microbial communities in desert steppe, and low and mediate N additions (30 and 50 kg N/(hm2•a)) had a promoting effect on them. The variation pattern of plant Shannon index was consistent with that of the soil bacterial Chao1 index. N deposition significantly affected the beta-diversity of plants and soil bacteria, but did not significantly affect fungal communities. In conclusion, N deposition led to co-evolution between desert steppe plants and soil bacterial communities, while fungal communities exhibited strong stability and did not undergo significant changes. These findings help clarify atmospheric N deposition effects on the ecological health and function of the desert steppe.

Biochar Application Reduces Saline–Alkali Stress by Improving Soil Functions and Regulating the Diversity and Abundance of Soil Bacterial Community in Highly Saline–Alkali Paddy Field

Saline–alkali soils seriously restrict the soil functions and the growth and diversity of soil microorganisms. Biochar can alleviate the negative effects of saline–alkali stress. However, it remains unclear how biochar reduces saline–alkali stress by improving soil functions and regulating the abundance and diversity of the soil bacterial community in highly saline–alkali paddy fields. To address this, a paddy field experiment was conducted in a highly saline–alkali paddy field using two nitrogen application levels (0 and 225 kg ha−1) and four biochar application rates (0, 1.5%, 3.0%, and 4.5% biochar, w/w). The results show that, compared with C0, biochar application, especially when combined with N fertilizer, significantly decreased the soil pH, exchangeable sodium percentage (ESP), saturated paste extract (ECe), and sodium adsorption ratio (SAR) while significantly increasing cation exchange capacity (CEC). These indicated that biochar can effectively reduce saline–alkali stress. Biochar application significantly increased soil content of total nitrogen (TN), alkali-hydrolysable N (AN), available P (AP), available K (AK), soil organic matter (SOM), and soil C/N ratio, both with or without N fertilization. Furthermore, biochar application further increased the relative abundance of bacterial communities and modified the bacterial community structure in highly saline–alkali paddy soils. Under C3N2, C2N2, and C1N2, Chao1 increased by 10.90%, 10.42%, and 1.60% compared to C0N2. Proteobacteria, Bacteroidetes, and Chloroflexi were the top three phyla in bacterial abundance. Biochar significantly increased the abundance of Proteobacteria while reducing Bacteroidetes and Chloroflexi, regardless of N fertilization. Correlation analysis results showed that the improvements in soil chemical and saline–alkali properties, as well as nutrient bioavailability after biochar application, had a positive effect on bacterial communities in highly saline–alkali paddy soils.

Fulvic acid modified ZnO nanoparticles improve nanoparticle stability, mung bean growth, grain zinc content, and soil biodiversity

Zinc oxide nanoparticles (ZnO NPs) have emerged as a novel solution to combat Zn deficiency in agriculture. However, challenges persist regarding their Zn utilization efficiency and environmental impact. Fulvic acid (FA), as a relatively mature modified material, is a promising candidate to enhance the environmental stability of ZnO NPs. This study investigates modifying ZnO NPs with FA to improve their stability and increase Zn content in mung bean fruit and explores their effect on plants and the soil ecosystem. We combined FA and ZnO NPs (FZ-50) at mass ratios of 1: 5, 1: 2, and 4: 5, denoted as 20 % FZ, 50 % FZ, and 80 % FZ, respectively. Initial germination tests revealed that the 50 % FZ treatment improved sprout growth and Zn content and minimized agglomeration the most. A subsequent pot experiment compared FZ-50 with ZnO, ZnO NPs, and F + Z (1: 1 FA: ZnO NPs). Notably, the FZ-50 treatment (50 % FZ applied to the soil) demonstrated superior results, exhibiting a 30.25 % increase in yield, 121 % improvement in root nodule quality, and 56.38 % increase in Zn content, with no significant changes in enzyme activities (catalase and peroxidase). Furthermore, FZ-50 increased soil available Zn content and promoted soil microorganism diversity, outperforming ZnO and ZnO NPs. This study underscores the potential of FA as a relatively mature material for modifying ZnO NPs to increase grain Zn content, presenting a novel approach to addressing Zn deficiency in agriculture.

Effects of Nano-zero-valent Iron and Earthworms on Soil Physicochemical Properties and Microecology in Cadmium-Contaminated Soils

The capacity of nano-zero-valent iron (nZVI) and soil animals to remediate heavy metal–contaminated soil has been widely studied. However, the synergistic effect of soil animals and nZVI has not been thoroughly investigated. Here, we studied the combined effect of earthworms and nZVI on soil physicochemical properties and microecology during remediation of cadmium (Cd)–contaminated soil. The results showed that although amendment with nZVI reduced earthworm survival and biomass, the combination of nZVI and earthworms was effective at reducing the available Cd (ACd) content of soil and improving its quality. ACd most effectively reduced by 75.3% in the presence of earthworms under the 0.25% nZVI combination. Meanwhile, the combined action of earthworms and nZVI significantly improved soil properties and increased the diversity of soil microorganisms. In the earthworm-free system, nZVI reduced ACd by increasing soil pH and the abundance of Stenotrophobacter in Cd-contaminated soil, in addition to the co-precipitation and adsorption reported in previous studies. Correlation analysis revealed that the combination of nZVI and earthworms synergistically decreased ACd by decreasing soil OM and increasing the relative abundance of Opitutus and Gemmatta. Overall, our study indicates that the combination of nano-zero-valent iron and earthworms is a potential system for in situ remediation of Cd-contaminated soils and provides a deep understanding of the mechanisms involved in remediation.

Unveiling the synergistic mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation for enhanced phenanthrene degradation in oil-contaminated soils

Autochthonous bioaugmentation and nutrient biostimulation are promising bioremediation methods for polycyclic aromatic hydrocarbons (PAHs) in contaminated agricultural soils, but little is known about their combined working mechanism. In this study, a microcosm trial was conducted to explore the combined mechanism of autochthonous fungal bioaugmentation and ammonium nitrogen biostimulation, using DNA stable-isotope-probing (DNA-SIP) and microbial network analysis. Both treatments significantly improved phenanthrene (PHE) removal, with their combined application producing the best results. The microbial community composition was notably altered by all bioremediation treatments, particularly the PHE-degrading bacterial and fungal taxa. Fungal bioaugmentation removed PAHs through extracellular enzyme secretion but reduced soil microbial diversity and ecological stability, while nitrogen biostimulation promoted PAH dissipation by stimulating indigenous soil degrading microbes, including fungi and key bacteria in the soil co-occurrence networks, ensuring the ecological diversity of soil microorganisms. The combination of both approaches proved to be the most effective strategy, maintaining a high degradation efficiency and relatively stable soil biodiversity through the secretion of lignin hydrolytic enzymes by fungi, and stimulating the reproduction of soil native degrading microbes, especially the key degraders in the co-occurrence networks. Our findings provide a fresh perspective of the synergy between fungal bioaugmentation and nitrogen biostimulation, highlighting the potential of this combined bioremediation approach for in situ PAH-contaminated soils.

Effects of repeated afidopyropen treatment on the structure and function of the soil microbial community

Chemical insecticides are the most effective pest control agents. Afidopyropen is a novel insecticide used against sap-sucking insects, such as aphids. However, the effects of repeated afidopyropen application on the structure and function of soil microorganisms remain unknown. In this study, the changes in the enzyme activities, community structure and function, and relative abundance of antibiotic resistance ontology (ARO) of soil microorganisms were investigated during three repeated afidopyropen applications under laboratory conditions at the maximum recommended dosage (M1) and 10 times the M1 (M10). The neutral phosphatase (NPA) and catalase (CAT) activities in the soil were significantly suppressed after afidopyropen treatment. The Simpson diversity index (1/D) and Shannon–Wiener diversity index (H) also decreased in both the M1 and M10 afidopyropen-treated soils, indicating a remarkable decrease in soil microorganism diversity. The average well color development (AWCD) first increased and subsequently recovered to normal levels after the third application of the insecticide, suggesting that afidopyropen application could increase the metabolic activity of soil microorganisms. Metagenomic analysis showed that repeated afidopyropen application in both the M1 and M10 treatment groups altered the community structure of soil microorganisms, albeit in different ways. Furthermore, repeated afidopyropen application significantly increased the relative ARO abundance, especially in the M10 treatment, with the most dominant AROs being adeF, baeS, and IND-6. These findings reveal the effects of excessive afidopyropen application on soil microorganisms and lay an important foundation for the comprehensive evaluation of the impact of this insecticide on the environment.

Environmental factors influencing the diversity and distribution of dictyostelid cellular slime molds in forest and farmland soils of western China.

Soil protists are an essential yet seriously understudied component of the soil microbiome. In this study, 11 new records of dictyostelids belonging to 2 orders, 3 families, and 4 genera were identified from 99 soil samples collected from different elevations and habitats in central Gansu and the southeastern and southcentral portions of Guizhou Province, China. We found that dictyostelid communities were significantly different between Gansu and Guizhou Provinces, apparently in response to different environmental factors. Moreover, dictyostelids were found to have the highest species diversity in mixed forests. Soil pH, temperature, and elevation were determined to be the primary factors that affect the distribution and occurrence of dictyostelids in Guizhou and Gansu Provinces. This work supplements the survey data available for dictyostelids elsewhere in China. These new findings have significant implications for our understanding of the diversity of soil microorganisms.

Soil Microbiome: Diversity, Benefits and Interactions with Plants

Plant roots aid the growth and functions of several kinds of microorganisms such as plant growth-promoting rhizobacteria, mycorrhizal fungi, endophytic bacteria, actinomycetes, nematodes, protozoans which may impart significant impacts on plant health and growth. Plant soil–microbe interaction is an intricate, continuous, and dynamic process that occurs in a distinct zone known as the rhizosphere. Plants interact with these soil microbes in a variety of ways, including competitive, exploitative, neutral, commensal, and symbiotic relationships. Both plant and soil types were found to have an impact on the community diversity and structure of the rhizosphere, or vice versa. The diversity of microorganisms in soil is thought to be essential for the management of soil health and quality because it has different plant growth-promoting or biocontrol effects that could be very advantageous for the host plant and alter plant physiology and nutrition. The composition of microbial community is influenced by soil and plant type. Besides these beneficial microbes, the soil also harbors microorganisms that are detrimental to plants, competing for nutrients and space, and causing diseases. Numerous microorganisms have antagonistic activity and the ability to defend plants from soil-borne diseases. The study of the soil microbiome is essential for formulating strategies for transforming the rhizosphere to the benefit of the plants. This review pays special emphasis on the types of microbial populations in the soil and how they influence plant growth, nutrient acquisition, inter-relationships between soil microbes and plants, stress resistance, carbon sequestration, and phytoremediation.

Organic management increases beneficial microorganisms and promotes the stability of microecological networks in tea plantation soil.

Organic agriculture is highly regarded by people for its commitment to health, ecology, care, and fairness. The soil microbial community responds quickly to environmental changes and is a good indicator for evaluating soil microecology. Therefore, from the perspective of soil microbial communities, elucidating the impact of organic management on soil microecology in tea plantations has great significance for improving local tea plantation systems. The study collected bulk soil from organic management (OM) and conventional management (CM) tea plantations in Pu'er City, a major tea-producing area in China, and analyzed their species diversity, structural composition, and co-occurrence networks using metagenomics technology. Compared with CM, the diversity index (Shannon) and evenness index (Heip) of soil fungi increased by 7.38% and 84.2% in OM tea plantations, respectively. The relative abundance of microorganisms related to the nitrogen cycle increased. Specifically, there was a significant increase in Rhodobiales, a 2-fold increase in Nitrospirae, and approximately 1.95 and 2.03 times increases in unclassified genera within Betaproteobacteria and Deltaproteobacteria, respectively. The relative abundance of plant residue degradation species, Gemmatimonadetes, Ascomycota, and Basidiomycota, increased by 2.8, 1, and 1.4 times, respectively. The OM was conducive to the establishment of collaborative relationships among bacterial species and increased the diversity and complexity of species relationships in fungal communities. The network stability of soil ecosystems was promoted. The organic tea plantations' keystone taxa contained mycorrhizal fungi (Pezoloma_ericae, Rhizophagus_irregularis, Rhizophagus_clarus), as well as species involved in soil nitrogen metabolism (Acidobacteria_bacterium, Acidobacteriia_bacterium_AA117, Sphingomonas_sp._URHD0007, Enhydrobacter_aerosaccus), pathogen (Erysiphe_pulchra), and parasites (Paramycosporidium saccamoeba). The partial least squares method (PLS-SEM) indicated that OM affected N-NH negatively, increasing the abundance of fungi, and thereby positively affecting the Shannon index. In brief, reasonable organic management can improve the diversity of soil microorganisms, increase the relative abundance of beneficial bacteria in tea plantation soil, and promote the stability of the soil microbial ecological network.

Bacterial abundance of cacao agroforestry, cacao monoculture and secondary forest land uses in north Luwu, South Sulawesi

Expanding the agricultural sector in North Luwu influences land use modification to enhance plantation output. Continuous land use and clearance can jeopardize the survival of native land vegetation, altering C and N cycles, community composition, population, and soil microbial activity. Microorganisms are essential for maintaining the health and quality of the soil. The abundance of soil microorganisms significantly impacts ecosystem function, so it can help boost agricultural output. This demonstrates that data on the abundance and diversity of soil microorganisms can be used to determine soil fertility. However, more information is needed about the diversity of soil microbes in North Luwu. This study seeks to determine the abundance of soil microorganisms, particularly for various land uses. Random soil samples were collected from cacao monoculture, cacao agroforestry, and secondary forest. The C: N ratio and the total number of microorganisms were then measured in the collected soil samples. Cacao agroforestry with the highest C: N ratio had 1.8 x 108 CFU/g of total soil bacterial, the highest bacterial abundance among the three land covers, followed by secondary forest and cacao monoculture with the lowest C: N ratio and lowest bacterial abundance 2 x 107 CFU/g. These results indicated that the soil C: N ratio influences the bacterial abundance of various land uses. The highest abundance of nitrate-fixing bacteria was found in secondary forests and the lowest in cacao agroforestry, even though the %N indicated by both was the same.

Weathering and soil production under trees growing on sandstones – The role of tree roots in soil formation

Rock weathering drives both landform formation and soil production/evolution. The less studied biological component of weathering and soil production caused by tree root systems is the main focus of the present study. Weathering by trees, which likely has been important in soil formation since the first trees emerged in the middle and late Devonian, is accomplished through both physical and biological means, like acids excreted by plants and exudates from associated bacterial communities. However, these processes are relatively poorly known. We assessed the impact of tree roots and associated microbiota on the potential level of biological weathering. Three research plots were selected in two sandstone regions in Poland. Two plots were in the Stołowe Mountains (Złotno, Batorów), a tableland built of Cretaceous sandstones. The third plot (Żegiestów) was in the Sącz Beskidy Mountains, the Carpathians. Soil samples were taken from tree root zones of Norway spruces from predefined sampling positions. Soils from non-tree control positions were also sampled. Soil samples were a subject of laboratory analyses which included the content of Fe and Al (amorphous and labile forms), carbon (C), nitrogen (N), and soil pH. The microbial functional diversity of soil microorganisms was determined using the Biolog (EcoPlate) system. Rock fragments were collected for mineralogical and a subject of optical microscopy and cathodoluminescence analyses in order to examine their mineralogical composition.Significant differences (pHolm-corrected < 0.05) between sample locations were found mostly for the Żegiestów plot: Soils at control positions differed from the crack and bulk soil sample positions in terms of C, N, C/N, and pH.Tree roots were able to develop a great variety of sizes and forms by following the existing net of bedrock discontinuities and hillslope microrelief. They developed along the most accessible surfaces, and caused rockcliff retreat and scree slope formation. These two features can be considered as initial stages of soil production. Trees add to the complexity of the soil system and allow formation of rhizospheric soils, and horizons rich in organic matter which are zones of a high microbial activity. However, as our study shows, rock cracks with roots cannot be considered as zones of microbial weathering. In addition, C content and microbial activity decreases with depth but can stay on a high level along living and dead roots. When entering rock fractures, they change the intensity of biomechanical weathering and soil properties. The highest biological activity of microorganisms was found in the control samples.Overall, tree roots do change the pattern of soil formation and explain the existing pattern of soil chemical properties, microbial activity, and potentially biological weathering intensity, and the intensity of those processes in correlation with root presence varies in space.

Effects of long-term herbaceous plant restoration on microbial communities and metabolic profiles in coal gangue-contaminated soil

The soil microbial diversity in the gangue accumulation area is severely stressed by a variety of heavy metals, while the influence of long-term recovery of herbaceous plants on the ecological structure of gangue-contaminated soil is to be explored. Therefore, we analysed the differences in physicochemical properties, elemental changes, microbial community structure, metabolites and expression of related pathways in soils in the 10- and 20-year herbaceous remediation areas of coal gangue. Our results showed that phosphatase, soil urease, and sucrase activities of gangue soils significantly increased in the shallow layer after herbaceous remediation. However, in zone T1 (10-year remediation zone), the contents of harmful elements, such as Thorium (Th; 1.08-fold), Arsenic (As; 0.78-fold), lead (Pb; 0.99-fold), and uranium (U; 0.77-fold), increased significantly, whereas the soil microbial abundance and diversity also showed a significant decreasing trend. Conversely, in zone T2 (20-year restoration zone), the soil pH significantly increased by 1.03- to 1.06-fold and soil acidity significantly improved. Moreover, the abundance and diversity of soil microorganisms increased significantly, the expression of carbohydrates in soil was significantly downregulated, and sucrose content was significantly negatively correlated with the abundance of microorganisms, such as Streptomyces. A significant decrease in heavy metals was observed in the soil, such as U (1.01- to 1.09-fold) and Pb (1.13- to 1.25-fold). Additionally, the thiamin synthesis pathway was inhibited in the soil of the T1 zone; the expression level of sulfur (S)-containing histidine derivatives (Ergothioneine) was significantly up-regulated by 0.56-fold in the shallow soil of the T2 zone; and the S content in the soil significantly reduced. Aromatic compounds were significantly up-regulated in the soil after 20 years of herbaceous plant remediation in coal gangue soil, and microorganisms (Sphingomonas) with significant positive correlations with benzene ring-containing metabolites, such as Sulfaphenazole, were identified.

Effects of multi-heavy metal composite pollution on microorganisms around a lead-zinc mine in typical karst areas, southwest China

Heavy metal pollution poses a serious hazard to the soil bacterial community. The purpose of this study is to understand the characteristics of soil heavy metal pollution in lead-zinc mines in karst areas and the response of Pb, Zn, Cd, and As-induced composite pollution to soil microorganisms. This paper selected soil samples from the lead-zinc mining area of Xiangrong Mining Co., Ltd., Puding County, Guizhou Province, China. The soil in the mining area is contaminated by multiple heavy metals such as Pb, Zn, Cd and As. The average levels of Pb, Zn, Cd and As in the Pb-Zn mining soil were 14.5, 7.8, 5.5 and 4.4 times higher than the soil background in this area, respectively. Bacterial community structures and functions were analyzed using 16 S rRNA high-throughput sequencing technology and the PICRUSt method. A total of 19 bacterial phyla, 34 classes and 76 orders were detected in the tested soil. At the phylum level, the Proteobacteria are the dominant flora of the soil in the tailings reservoir area of the lead-zinc mine, respectively GWK1 (49.64%), GWK2 (81.89%), GWK3 (95.16%); and for the surrounding farmland soil, the Proteobacteria, Actinobacteriota, Acidobacteriota, Chloroflexi and Firmicutes are the most abundant in five bacterial groups. RDA analyses revealed that the heavy metal pollution of the lead-zinc mining area has a significant impact on the diversity of soil microorganisms. As the distance from the mining area increased, the heavy metal comprehensive pollution and potential risk value decreased, and the bacterial diversity increased. Additionally, various types of heavy metals have different effects on bacterial communities, and soil heavy metal content will also change the bacterial community structure. Proteobacteria positively related to Pb, Cd, and Zn, therefore, Proteobacteria were highly resistant to heavy metals. PICRUSt analysis suggested that heavy metals significantly affect the metabolic function of microorganisms. Microorganisms might generate resistance and enable themselves to survive by increasing the transport of metal ions and excreting metal ions. These results can be used as a basis for the microbial remediation of heavy metal-contaminated farmland in mining areas.