Soil Community Composition Research Articles

Plant colonizers of a mercury contaminated site: trace metals and associated rhizosphere bacteria

Background and aimsMercury (Hg) contamination poses severe human and environmental health risks. We aimed to evaluate the colonization of Hg-contaminated sites by native plants and the prokaryotic composition of rhizosphere soil communities of the dominant plant species.MethodsA field study was conducted at a Hg-contaminated site in Romania. Metal concentrations in soil and plant samples were analyzed using portable X-ray fluorescence spectrometry. The prokaryotic composition of rhizosphere soil communities was determined through 16S rRNA amplicon sequencing and community functionality was predicted through PICRUSt2.ResultsSite-specific trace metal distribution across the site drove plant species distribution in the highly contaminated soil, with Lotus tenuis and Diplotaxis muralis associated with higher Hg concentrations. In addition, for the bacterial communities in the rhizosphere soil of D. muralis, there was no observable decrease in alpha diversity with increasing soil Hg levels. Notably, Actinomycetota had an average of 24% relative abundance in the rhizosphere communities that also tested positive for the presence of merA, whereas in the absence of merA the phylum’s relative abundance was approximately 2%. merA positive rhizosphere communities also displayed an inferred increase in ABC transporters.ConclusionsThe results suggest a dependence of species-wise plant survival on local trace metal levels in soil, as well as an intricate interplay of the latter with rhizosphere bacterial diversity. Knowledge of these interdependencies could have implications for phytoremediation stakeholders, as it may allow for the selection of plant species and appropriate soil microbial inoculates with elevated Hg tolerance.

High soil moisture rather than drying-rewetting cycles reduces the effectiveness of nitrification inhibitors in mitigating N2O emissions

Climate change has been intensifying soil drying and rewetting cycles, which can alter the soil microbiome structure and activity. Here we hypothesized that a soil drying-rewetting cycle enhances biodegradation and, hence, decreases the effectiveness of nitrification inhibitors (NIs). The effectiveness of DMPP (3,4-Dimethylpyrazole phosphate) and MP + TZ (3-Methylpyrazol and Triazol) was evaluated in 60-day incubation studies under a drying and rewetting cycle relative to constant low and high soil moisture conditions (40% and 80% water-holding capacity, WHC, respectively) in two different textured soils. The measurements included (i) daily and cumulative N2O-N emissions, (ii) soil NH4+-N and NO3−-N concentrations, and (iii) the composition of bacterial soil communities. Application of DMPP and MP + TZ reduced the overall N2O-N emissions under drying-rewetting (-45%), as well as under 40% WHC (-39%) and 80% WHC (-25%). DMPP retarded nitrification and decreased N2O-N release from the sandy and silt loam soils, while MP + TZ mitigated N2O-N production only from the silt loam soil. Unexpectedly, between days 30 and 60, N2O-N emissions from NI-treated soils increased by up to fivefold relative to the No-NI treatment in the silt loam soil at 80% WHC. Likewise, the relative abundance of the studied nitrifying bacteria indicated that the NIs had only short-term effectiveness in the silt loam soil. These results suggested that DMPP and MP + TZ might trigger high N2O-N release from fine-textured soil with constant high moisture after this short-term inhibitory effect. In conclusion, DMPP and MP + TZ effectively reduce N2O-N emissions under soil drying and rewetting.

Virus decay and community composition in virus-amended sterile soil under slurry and unsaturated conditions

Soil viruses are abundant and diverse. The available research suggests viruses play a significant role in shaping the structure and function of soil microbial communities. Their effects are modulated by various environmental factors, including soil temperature, moisture, and geochemical conditions. This study investigated the persistence/inactivation of naturally occurring soil viruses added to sterilized soil, providing insights into virus decay under abiotic conditions. Soil microcosm experiments under saturated (slurry) conditions (5 g:12 mL) and unsaturated conditions (60% of field capacity) revealed a consistent decline in viral abundance over time. Under saturated conditions, there was a reduction of over 90% in viral abundance after 10 d, a steeper decline than the 55% reduction observed under unsaturated conditions during the same length of incubation. Notably, the composition of viruses also changed over time, and the remaining viruses demonstrated infectious capabilities for up to 13 d in saturated and 16 d in unsaturated soil, evidenced by changes in viral abundance upon the addition of live bacteria. Introducing live bacteria reduced the net viral dissipation in saturated soil but resulted in a net increase in viral abundance in unsaturated soil from 4.49 × 108 to 6.76 × 109 within 3 days. The increase in viral abundance in the unsaturated soil was partly due to the emergence of new viruses from prophage induction. This research presents a preliminary exploration into extracellular persistence of soil viruses under varying moisture conditions.

Consecutive Fertilization-Promoted Soil Nutrient Availability and Altered Rhizosphere Bacterial and Bulk Fungal Community Composition

Fertilization is an important measure to quickly supplement the soil nutrients required for plantation productivity. However, the response patterns of the microbial community and functional taxa in Larix plantation root, rhizosphere, and bulk soil to short-term and consecutive fertilization have rarely been reported. In this study, we assessed Larix root, rhizosphere, and bulk soil microbial community on days 0, 5, 15, and 30 after the first inorganic fertilization and after three consecutive years of fertilization. The bacterial 16S and fungal ITS high-throughput sequencing technology were used to monitor changes in microbial community composition and potential functional groups, as well as changes in soil nutrient content and enzyme activity to evaluate the status of plantation soil productivity. Consecutive fertilization treatment significantly increased the available nitrogen, phosphorus, and potassium (NPK) content and soil enzyme activity. The nonmetric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) results showed that there were significant differences in microbial community composition in root samples, rhizosphere soil, and bulk soil samples. The dominant microbial taxa were different between root and soil microbial community composition. Consecutive fertilization treatment had little effect on endophytic microbial community but significantly increased the abundance of Gaiellales in rhizosphere soil and Mortierella in bulk soil. The redundancy analysis (RDA) and co-occurrence network analyses showed that Gaiellales and Mortierellales had significant positive correlations with soil nutrient content and enzyme activity. The fungal functional group compositions were significantly affected by consecutive fertilization treatment and the proportions of ectomycorrhizal and saprotroph significantly decreased, but the proportion of endophyte significantly increased in bulk soil samples. Our results suggested that consecutive fertilization may promote soil nutrient availability by increasing the abundance of Gaiellales and Mortierella. Consecutive fertilization maintained the balance of the soil microbiota under Larix plantation and had a positive effect on promoting soil nutrient availability. This study provided a theoretical basis for consecutive fertilization to promote soil nutrient availability through specific microbial groups.

Water table depth and plant species determine the direction and magnitude of methane fluxes in floodplain meadow soils.

Methane (CH4) is a powerful greenhouse gas with ongoing efforts aiming to quantify and map emissions from natural and managed ecosystems. Wetlands play a significant role in the global CH4 budget, but uncertainties in their total emissions remain large, due to a combined lack of CH4 data and fuzzy boundaries between mapped ecosystem categories. European floodplain meadows are anthropogenic ecosystems that originated due to traditional management for hay cropping. These ecosystems are seasonally inundated by river water, and straddle the boundary between grassland and wetland ecosystems; however, an understanding of their CH4 function is lacking. Here, we established a replicated outdoor floodplain-meadow mesocosm experiment to test how water table depth (45, 30, 15 cm below the soil surface) and plant composition affect CH4 fluxes over an annual cycle. Water table was a major controller on CH4, with significantly higher fluxes (overall mean 9.3 mg m-2 d-1) from the high (15 cm) water table treatment. Fluxes from high water table mesocosms with bare soil were low (mean 0.4 mg m-2 d-1), demonstrating that vegetation drove high emissions. Larger emissions came from high water table mesocosms with aerenchymatous plant species (e.g. Alopecurus pratensis, mean 12.8 mg m-2 d-1), suggesting a role for plant-mediated transport. However, at low (45 cm) water tables A. pratensis mesocosms were net CH4 sinks, suggesting that there is plasticity in CH4 exchange if aerenchyma are present. Plant cutting to simulate a hay harvest had no effect on CH4, further supporting a role for plant-mediated transport. Upscaling our CH4 fluxes to a UK floodplain meadow using hydrological modelling showed that the meadow was a net CH4 source because oxic periods of uptake were outweighed by flooding-induced anoxic emissions. Our results show that floodplain meadows can be either small sources or sinks of CH4 over an annual cycle. Their CH4 exchange appears to respond to soil temperature, moisture status and community composition, all of which are likely to be modified by climate change, leading to uncertainty around the future net contribution of floodplain meadows to the CH4 cycle.

Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India.

In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.

Influence of weeding methods on rhizosphere soil and root endophytic microbial communities in tea plants.

Polyethylene mulch is a kind of inorganic mulch widely used in agriculture. The effects of plastic mulch debris on the structure of plant soil and root growth have been fully studied, but their effects on endophytic microbial communities have not been explored to a large extent. In this study, High-throughput sequencing of bacterial 16S rRNA genes and fungal ITS region sequences were used to analyze microbial community structure and composition in rhizosphere soil and root endophytic of tea plant under three different weeding methods: polyethylene mulching, hand weeding and no weeding (CK). The results showed that the weeding methods had no significant effect on the rhizosphere and root endophytic microbial abundance, but the rhizosphere bacterial structure covered by polyethylene mulch was significantly different than hand weeding and CK. The rhizosphere fungal diversity was also significantly higher than the other two analyzed treatments. The community abundance of rhizosphere microorganisms Acidobacteria, Candidatus Rokubacteria and Aspergillus covered by polyethylene mulch decreased significantly, whereas Bradyrhizobium, Solirubrobacterales and Alphaproteobacteria increased significantly. The abundance of bacteria Ktedonobacter, Reticulibacter, Ktedonosporobacter and Dictyobacter communities covered by polyethylene mulch was significantly changed, and the abundance of Fusarium and Nitrobacteraceae was significantly increased. Rhizosphere dominant bacteria were negatively correlated with soil available nitrogen content, while dominant fungi were significantly correlated with soil pH, total nitrogen and total potassium. Polyethylene mulch forms an independent micro-ecological environment. At the same time, the soil nutrient environment was enriched by affecting the nitrogen cycle, and the composition of microbial community was affected. This study elucidated the effects of polyethylene mulch on soil microbial community in tea garden and provided a new theoretical understanding for weed management.

Connecting competitor, stress-tolerator and ruderal (CSR) theory and Lund Potsdam Jena managed Land 5 (LPJmL 5) to assess the role of environmental conditions, management and functional diversity for grassland ecosystem functions

Abstract. Forage offtake, leaf biomass and soil organic carbon storage are important ecosystem services of permanent grasslands, which are determined by climatic conditions, management and functional diversity. However, functional diversity is not independent of climate and management, and it is important to understand the role of functional diversity and these dependencies for ecosystem services of permanent grasslands, since functional diversity may play a key role in mediating impacts of changing conditions. Large-scale ecosystem models are used to assess ecosystem functions within a consistent framework for multiple climate and management scenarios. However, large-scale models of permanent grasslands rarely consider functional diversity. We implemented a representation of functional diversity based on the competitor, stress-tolerator and ruderal (CSR) theory and the global spectrum of plant form and function into the Lund Potsdam Jena managed Land (LPJmL) dynamic global vegetation model (DGVM) forming LPJmL-CSR. Using a Bayesian calibration method, we parameterised new plant functional types (PFTs) and used these to assess forage offtake, leaf biomass, soil organic carbon storage and community composition of three permanent grassland sites. These are a temperate grassland and a hot and a cold steppe for which we simulated several management scenarios with different defoliation intensities and resource limitations. LPJmL-CSR captured the grassland dynamics well under observed conditions and showed improved results for forage offtake, leaf biomass and/or soil organic carbon (SOC) compared to the original LPJmL 5 version at the three grassland sites. Furthermore, LPJmL-CSR was able to reproduce the trade-offs associated with the global spectrum of plant form and function, and similar strategies emerged independent of the site-specific conditions (e.g. the C and R PFTs were more resource exploitative than the S PFT). Under different resource limitations, we observed a shift in the community composition. At the hot steppe, for example, irrigation led to a more balanced community composition with similar C, S and R PFT shares of aboveground biomass. Our results show that LPJmL-CSR allows for explicit analysis of the adaptation of grassland vegetation to changing conditions while explicitly considering functional diversity. The implemented mechanisms and trade-offs are universally applicable, paving the way for large-scale application. Applying LPJmL-CSR for different climate change and functional diversity scenarios may generate a range of future grassland productivities.

Field application of hydroxyapatite and humic acid for remediation of metal-contaminated alkaline soil.

The quality of soil is essential for ensuring the safety and quality of agricultural products. However, soils contaminated with toxic metals pose a significant threat to agricultural production and human health. Therefore, remediation of contaminated soils is an urgent task, and humic acid (HA) with hydroxyapatite (HAP) materials was applied for this study in contaminated alkaline soils to remediate Cd, Pb, Cu, and Zn. Physiochemical properties, improved BCR sequential extraction, microbial community composition in soils with superoxide dismutase (SOD), peroxidase (POD), and chlorophyll content in plants were determined. Among the studied treatments, application of HAP-HA (2:1) (T7) had the most significant impact on reducing the active forms of toxic metals from soil such as Cd, Pb, Cu, and Zn decreased by 18.59%, 9.12%, 11.83%, and 3.33%, respectively, but HAP and HA had a minor impact on metal accumulation in Juncao. HAP (T2) had a beneficial impact on reducing the TCleaf/root of Cd, Cu, and Zn, whereas HAP-HA (T5) showed the best performance for reducing Cd and Cu in EFleaf/soil. HAP-HA (T5 and T7) showed higher biomass (57.3%) and chlorophyll (17.9%), whereas HAP (T4) showed better performance in POD (25.8%) than T0 in Juncao. The bacterial diversity in soil was increased after applying amendments of various treatments and enhancing metal remediation. The combined application of HAP and HA effectively reduced active toxic metals in alkaline soil. HAP-HA mixtures notably improved soil health, plant growth, and microbial diversity, advocating for their use in remediating contaminated soils.

Nitrogen-based fertilizers differentially affect protist community composition in paddy field soils

Nitrogen-based fertilizers differentially affect protist community composition in paddy field soils

Mechanisms and implications of bacterial-fungal competition for soil resources.

Elucidating complex interactions between bacteria and fungi that determine microbial community structure, composition, and functions in soil, as well as regulate carbon (C) and nutrient fluxes, is crucial to understand biogeochemical cycles. Among the various interactions, competition for resources is the main factor determining the adaptation and niche differentiation between these two big microbial groups in soil. This is because C and energy limitations for microbial growth are a rule rather than an exception. Here, we review the C and energy demands of bacteria and fungi-the two major kingdoms in soil-the mechanisms of their competition for these and other resources, leading to niche differentiation, and the global change impacts on this competition. The normalized microbial utilization preference showed that bacteria are 1.4-5 times more efficient in the uptake of simple organic compounds as substrates, whereas fungi are 1.1-4.1 times more effective in utilizing complex compounds. Accordingly, bacteria strongly outcompete fungi for simple substrates, while fungi take advantage of complex compounds. Bacteria also compete with fungi for the products released during the degradation of complex substrates. Based on these specifics, we differentiated spatial, temporal, and chemical niches for these two groups in soil. The competition will increase under the main five global changes including elevated CO2, N deposition, soil acidification, global warming, and drought. Elevated CO2, N deposition, and warming increase bacterial dominance, whereas soil acidification and drought increase fungal competitiveness.

Arbuscular mycorrhizal fungal communities in soils where astragalus had grown for 2 years were similar to those in the abandoned farmland.

Astragalus-cultivated soils are enriched in arbuscular mycorrhizal fungi (AMF); however, the community changes of AMF between years in stragalus-cultivated soils are still unclear. To illustrate this, using high-throughput amplicon sequencing and quantitative real-time PCR, we analyzed the AMF communities of the abandoned farmlands and interannual astragalus-cultivated soils for 1-, 2-, 3-, and 4-years, including community composition, dominant, core, specific and significantly fluctuating AMF, co-occurrence network, alpha diversity, and beta diversity. A total of 74 OTUs were classified into one phylum, Glomeromycota; one class, Glomeromycetes; four orders; four families; and six genera. The 2-year soil had the highest number of reads among the interannual soils. Only one OTU was shared among all interannual soils. The treatments significantly affected the Ace, Shannoneven, and Shannon estimators of the communities. The 2-year soil had the highest richness, evenness, and diversity among all interannual soils and was the closest to the abandoned farmland in terms of alpha diversity. Glomus of the family Glomeraceae was the dominant genus present in all treatments, and the composition of the dominant genus in interannual soils was different. Both Glomus and Diversispora were the core AMF in interannual soils, and specific AMF existed in different interannual soils. Glomus is a genus that exhibits significant interannual variation. The interannual time significantly affected the network connectivity. The results of the principal coordinate analysis showed that the community composition of the interannual soils was close to each other and separated from the abandoned farmland, and that the interannual time significantly affected the community composition. Among the interannual soils, the 2-year soil may be more suitable for A. sinensis seedling rotation.

Effects of salt stress on bacterial community composition and diversity in rhizosphere soil of Bletilla striata

Salinization environment affects the normal growth and development of plants, as well as the microbial community in the rhizosphere. To explore the succession dynamics of bacterial communities in the rhizosphere soil of Bletilla striata under salt stress condition, we performed 16S rRNA high-throughput sequencing to determine the bacterial community composition and diversity of B. striata in the rhizosphere under different salt stress concentrations, measured the effects of salt stress on the growth and development of B. striata and soil physicochemical pro-perties, and analyzed the correlation between community composition of rhizosphere bacteria and the soil environmental factors. The results showed that compared with the control, salt stress reduced growth rate and health degree of B. striata, and significantly decreased the content of soil organic matter, nitrogen and phosphorus. Under the salt stress treatment, species diversity and evenness of the bacterial communities in the rhizosphere of B. striata showed a trend of first decreasing and then increasing. There were significant differences in the relative abundance and variation trends of the dominant bacterial taxa in the rhizosphere soil of B. striata at the phylum and class levels between the control and the salt stress treatments. Salt stress intensity and duration were important factors affecting bacterial community composition in the rhizosphere soil of B. striata. Soil organic matter, available nitrogen, and total phosphorus content were key environmental factors affecting the structure of rhizosphere bacterial community composition. Functional genes related to cytoskeleton, cell motility, substance metabolism and signal transduction mechanisms may be involved in the adaptation and stress response of bacterial communities to salt stress. This study would provide theoretical basis and reference for the cultivation management of B. striatain saline area.

The Effect of Conventional and Conservative Tillage Systems on Microbial Community Composition and Physiological Activity in Soils from Bărăgan Plain

The paper aimed to present the results of research carried out on size, taxonomic composition and physiological activity of soil microbiota for assessing the effect of classic (conventional) and conservative (minimum tillage) agriculture systems applied in a zone affected by aridification from Bărăgan Plain. Significant differences concerning the quantitative parameters characterizing the bacterial and fungal communities from the two soil systems of tillage have been evidenced. Total counts of bacteria doubled and total counts of fungi was with one order of magnitude higher in soil minimum-tilled than in soil under conventional tillage system. Soil respiration values registered for both conservative and conventional systems are considered to characterize high levels of microbial physiological activities, with slightly higher values for minimum tillage system application than for conventional system. The beneficial effect of conservative system was evidenced by higher values of diversity indices registered for both bacterial and, especially fungal communities, as compared with those characterizing the communities from soil under conventional tillage system. The minimum tillage system favoured the increasing of abundance and diversity of actinomycetes, the dominance of Pseudomonas and Bacillus bacterial species and fungal species belonging to genera Aspergillus, Trichoderma, Mortierella and Paecilomyces in composition of soil microbiota, with multiple roles in main soil processes: decomposition of vegetal residues, synthesis of humus precursors, carbon sequestration, alleviation of various abiotic stress (drought, salinity), increasing accessibility of nutrients for plants, yields, biocontrol of plant pathogens.

Evergreen gymnosperm tree abundance drives ground beetle density and community composition in eastern US temperate forests

PurposeSoil invertebrates are abundant and diverse members of forest ecosystems, contributing in large parts to ecosystem functioning. Understanding drivers of soil invertebrate diversity, density, and community composition is critical to inform management practices as forests face rapid changes in land use and climate. Tree community metrics may help predict invertebrate communities due to their large role in shaping microhabitat and soil conditions. Ground beetles are a large family of soil-dwelling invertebrates comprised of multiple functional groups ideal for tying tree communities to invertebrate communities broadly. Methods Here, we evaluated the effects of tree diversity, density, and functional groups on ground beetle (Carabidae) diversity, density, and community composition in four eastern US temperate forest sites in the National Ecological Observatory Network. Results We found little evidence to support our hypothesis that higher tree diversity and density would, respectively, lead to higher diversity and density ground beetle communities. Instead, evergreen tree abundance strongly shaped ground beetle density and community composition. Specifically, evergreen stands contained a lower density of ground beetles than deciduous stands. Similarly, the relative abundance of predatory ground beetles increased as the relative abundance of evergreen trees increased. Conclusions Our results show that the resource environments created by trees with varying leaf habits are a dominant force driving ground beetle community diversity and density patterns and suggest that future research exploring mechanisms driving this pattern could improve our understanding of plant-soil interactions.

Straw incorporation and nitrogen fertilization enhance soil carbon sequestration by altering soil aggregate and microbial community composition in saline-alkali soil

Straw incorporation and nitrogen fertilization enhance soil carbon sequestration by altering soil aggregate and microbial community composition in saline-alkali soil

Changes in Soil Chemical Properties and Rhizosphere Bacterial Community Induced by Soil Amendments Associated with Reduction in Cadmium Accumulation by Rice

Soil amendments have been extensively employed for the purpose of remediating soils contaminated with cadmium (Cd). However, the potential impacts of soil amendments on soil chemical properties, soil Cd bioavailability, total Cd accumulation by rice, and rhizosphere bacterial community in Cd-contaminated paddy fields located in a tropical region is still at its infancy. In this study, a commercial MgO-CaO-SiO2 conditioner (A), biochar (B), and a combination of the commercial MgO-CaO-SiO2 conditioner and biochar with a ratio of 1:1 (C) were applied at two different doses [2250 kg ha−1 (A150, B150, C150), 4500 kg ha−1 (A300, B300, C300)] to investigate their impacts on soil Cd stabilization and total Cd uptake of rice straw and grain in a Cd-contaminated remediation field experiment. Rhizosphere bacterial community diversity and composition were also assessed using high-throughput sequencing based on 16S rRNA genes. Compared with non-amendment treatment (CK), soil pH, cation exchange capacity (CEC), organic matter (OM), total nitrogen (TN), available nitrogen (AN), and nitrate (NO3−) concentrations were significantly elevated, whereas ammonium (NH4+) and soil available Cd concentrations were reduced by soil amendment treatments. Meanwhile, soil amendments significantly decreased concentrations of total Cd in both rice straw and grain, with the lowest Cd concentration in the C300 treatment. Soil pH and CEC were significantly and negatively associated with soil Cd availability and rice straw and grain Cd concentrations, while NH4+ concentration was positively correlated with soil available Cd concentration, and OM, TN, and NO3− concentrations were positively linked with rice grain Cd concentration. Soil amendments significantly increased bacterial Chao 1 and Shannon indexes and altered bacterial community composition in rhizosphere soil, due to changes in the composition of the community primarily influenced by variations in soil pH, CEC, and soil available Cd, NH4+, available phosphorous (AP) and available Potassium (AK) concentrations. Furthermore, the abundant bacterial species (Pseudomonas) and rare bacterial species (Bacillus, Candidatus_Solibacter and Streptomyces) have been up-regulated by different soil amendments, which might be in favour of soil Cd immobilization. A structural equation model also showed that soil amendments could improve bacterial diversity and change soil pH and CEC, which were conducive to hindering the removal and conversion of Cd. Overall, these results indicate that biochar-(MgO-CaO-SiO2) mixed amendments at high dosage exerted better performance compared with single application soil amendment A and B. The changes in soil chemical properties, available Cd content, and rhizosphere bacterial community assembly induced by soil amendments are closely correlated with the decrease in rice’s ability to accumulate Cd.

Eucalyptus plantation reduces diversity and disrupts predator-prey correlations of soil invertebrates within Atlantic Forest

Human activities in the Anthropocene have led to the conversion of a significant area of the Earth's surface to agroecosystems, including tree plantations such as eucalyptus. Brazil, as the largest producer of eucalyptus timber, faces the challenge of preserving its rich biodiversity, particularly in the Atlantic Forest biome, which is one of the world's most threatened and diverse. This study aimed to assess the impact of eucalyptus plantation on soil invertebrate communities compared to that of native forest remnants. We sampled ants, beetles, springtails, and spiders as model groups to evaluate the alpha diversity and composition of soil invertebrates in these forests. We also examined trophic interactions between springtails and their potential natural enemies (spiders, ants, and beetles) in both environments. Our results revealed that the abundance and richness of ants and beetles were higher in native forests than in eucalyptus plantations, whereas springtails exhibited a negative response to eucalyptus plantation in terms of abundance, and spiders showed higher richness in eucalyptus plantations. Furthermore, the composition of soil invertebrate communities, with the exception of springtails, was significantly different between eucalyptus plantations and native forests.The correlations between the abundance of springtails and their potential predators (spiders and beetles) were significantly reduced in eucalyptus plantations compared with native forests. Our findings highlight the negative impact of eucalyptus plantation on soil invertebrate diversity and community composition, potentially disrupting predator-prey relationships and emphasizing the importance of preserving native forests to safeguard invertebrate biodiversity and ecological processes.

Microbial activity, community composition and degraders in the glyphosate-spiked soil are driven by glycine formation

Widely-used glyphosate may produce aminomethylphosphonic acid (AMPA), glycine and sarcosine. To date, little is known about effects of these degradation products on soil microorganisms and their potential degraders. Here, we incubated a soil spiked either with 2-13C-glyphosate, 13C-AMPA, 13C3-sarcosine or 13C2-glycine for 75 days. Respiration (CO2 tot) and mineralization rates of the compound (13CO2) were estimated in addition to phospholipid fatty acids (PLFAstot and 13C-PLFAs) as biomarkers to identify four groups of microorganisms (Gram-negative & Gram-positive bacteria, actinobacteria, fungi). 16S/ITS rRNA amplicon sequencing was also conducted to identify the microbial community at the phylum and genus level. The CO2 tot and 13CO2 rates were highest on day 2 in all treatments, as follows: glycine (CO2 tot: 1.09 μmol g−1; 13CO2: 18 %) > sarcosine (CO2 tot: 0.89 μmol g−1; 13CO2: 8.5 %) > glyphosate (CO2 tot: 0.67 μmol g−1; 13CO2: 2.2 %) > AMPA (CO2 tot: 0.53 μmol g−1; 13CO2: 0.3 %). Both the PLFAstot and 13C-PLFAs were highest in glycine (PLFAstot: 0.054–0.047 μmol g−1; 13C-PLFAs: 0.2–0.4 %) and glyphosate (PLFAstot: 0.049–0.047 μmol g−1; 13C-PLFAs: 0.1–0.3 %) treatments compared to sarcosine and AMPA treatments. Gram negative bacteria were major microbial group of soil microbiome as well as primary degraders of all compounds. In contrast, Gram-positive bacteria, actinobacteria and fungi could have been consumers of primary degraders. Certain genera e.g. Gemmatimonas, Arenimonas and Massilia showed increased abundance in certain treatments indicating their potential involvement in biodegradation. Based on similar time-dependent microbial activity and shifts in abundances of (13C-)PLFAs and 16S rRNA genera, we deduced that glyphosate was mainly degraded to glycine, and presumably at elevated amounts. We reported for the first time that the glycine presumably altered microbial activity and community composition rather than glyphosate directly. Future studies should thus also consider the potential impacts of degradation products of the parent compound on soil microbiomes.

Soil Microbial Community and Their Relationship with Soil Properties across Various Landscapes in the Mu Us Desert

Soil microorganisms play crucial roles in maintaining material circulation and energy flow in desert ecosystems. However, the structure and function of soil microorganisms in different forestlands are currently unclear, restricting the use of sand-fixing plants and the understanding of forest ecosystem functions. In this study, Artemisia ordosica, Caragana korshinskii, and Salix psammophila, three types of sand-fixing forests widely distributed in the Mu Us Sandy Land, were used to explore the effects of sand-fixing forests on soil physicochemical properties, soil enzyme activity, soil microbial biomass, microbial community structure, and inter-microbial species relationships. Soils of forestlands showed higher soil organic carbon (SOC), total phosphorus (TP), and total nitrogen (TN) contents than bare sandy land. The SOC in bare sandy soil was only 0.84 g kg−1, while it remained 1.55–3.46 g kg−1 in forestland soils. The TN in bare sandy land soil was 0.07 g kg−1, which was significantly lower than that in forestland soils (0.35–0.51 g kg−1). The TP in bare sandy soil was 0.18 g kg−1, significantly lower than that in forestland soils (0.46–0.69 g kg−1). Afforestation of bare sandy land improved soil microbial carbon and nitrogen contents and increased microbial enzyme activities of acid phosphatase and N-acetyl-β-D-glucosaminidase. Significant differences were observed between the three forestlands and bare sandy land in terms of soil microorganisms and community composition. With the establishment of a sand-fixing forest, the alpha diversity of soil bacteria significantly improved, whereas that of soil fungi remained stable. The bacterial community comprised 33 phyla, 106 classes, 273 orders, 453 families, and 842 genera. While five fungal phyla were detected by OTUs at a similarity of 97%, bacterial and fungal community structures were affected by the organic carbon content, sand particle content, soil pH, total nitrogen, and total phosphorus contents of soils. This study is helpful for vegetation construction and protection on sandy lands from the perspective of plant-microbe interactions.