Community Function Research Articles

Impact of dual Bt-transgenic maize (2A7) on soil microbial communities and enzyme activities: A comparative study with control variety Z58

The impacts of transgenic crops on soil microbiology and fertility are critical in determining their biosafety. While transgenic crops can alter soil microbes, their effects are often context-dependent; therefore, the ecological importance of these changes remains a topic of ongoing research. Using high-throughput sequencing, we investigated the effects of Bacillus thuringiensis (Bt) maize expressing the mcry1Ab and mcry2Ab genes (2A7) on soil nutrient dynamics, as well as the diversity and function of soil microbial communities, including bacteria and fungi, within different soil compartments. Our findings revealed a plant-shaped rhizosphere (RS) microbial community as a result of the selective recruitment of microorganisms from the surrounding environment. The transgene insertion had a significant impact on the RS niche, and several species eventually became associated with Z58 and 2A7 plants. For example, Neocosmospora rubicola fungal and Pantoea dispersa bacterial microorganisms were significantly decreased in the dual Bt-transgenic 2A7 rhizosphere but enriched in the Z58 rhizospheres. The activity of soil enzymes such as urease, invertase, and alkaline phosphatase was boosted by Bt-transgenic 2A7. LefSe analysis identified significant bacterial and fungal biomarker species that were responsible for the differential effects of Bt-transgenic 2A7 and control Z58 within rhizosphere soils. Mantel analysis further demonstrated that the root exudates of 2A7 altered nutrient-acquisition enzymes by influencing biomarker taxa. PICRUSt2 functional characterization revealed a significantly higher abundance of the phosphate-starvation-inducible protein in control Z58 than in Bt-transgenic 2A7. Furthermore, taxonomy, alpha (Shannon diversity), and beta diversity analyses all revealed niche-driven microbial profile differentiation. Niche partitioning also had a significant impact on N- and P-related COGs as well. Our findings suggests that Bt-transgenic 2A7 modulates rhizosphere microbial communities by affecting biomarker taxa and soil enzyme activity. These findings will promote sustainable agriculture practices by advancing our knowledge of the ecological effects of Bt crops on soil microbial communities.

Investigation of the effects of polyethylene microplastics at environmentally relevant concentrations on the plant-soil-microbiota system: A two-year field trial

Microplastics are a potential threat to agricultural sustainability. However, the effects of microplastics at environmentally relevant concentrations on the plant-soil-microbiota system in realistic field conditions are largely unknown. Herein, we conducted a two-year field trial to study the effects of polyethylene (PE) microplastics at 0, 100, and 600 mg/kg on crop growth, soil properties, and the composition and function of microbial communities in a farmland with rice-wheat rotation. PE did not affect wheat growth but it increased the rice grain weight by 42.5 % at 600 mg/kg, and enhanced rice height by 35.4 % and 30.2 % at 100 and 600 mg/kg, respectively. The presence of PE significantly decreased soil available phosphorus during the wheat season, while it reduced soil total nitrogen, NH4+-N and available phosphorus during the rice season. There were five and sixteen bacterial orders identified changed by PE in wheat and rice soils, respectively. Specifically, PE at different concentrations differentially altered the abundances of sulfate-reducing bacteria Thermodesulfovibrionia, Thermoactinomycetales and Syntrophobacterales, and further modified soil sulfate respiration in wheat soils. During the rice season, PE (100 mg/kg) increased the abundance of Xanthomonadales by 98.0 % and enriched the functional groups of intracellular parasites, while PE (600 mg/kg) inhibited twelve cluster of orthologous group function classes and disturbed bacterial metabolism. This study suggests that PE exhibits a greater impact on the plant-soil-microbiota system during the rice season compared to the previous year's wheat season, highlighting the importance of crop type and cultivation practices in determining the environmental risks of microplastics in agroecosystems.

Response of Bacterial Community Structure and Function in Rhizosphere Soil on the Photosynthesis of Selected Plant Types C3 and C4 under Bis(2,4,6-tribromophenoxy) Ethane Exposure

This study investigated the response of a bacterial community’s structure and function in the rhizosphere soil of C3 and C4 plants under bis(2,4,6-tribromophenoxy) ethane (BTBPE) exposure. The bacterial community composition was determined using 16S rRNA sequencing, while FAPROTAX and PICRUSt 2 were employed for functional predictions. Results showed significant differences between C3 and C4 plants in terms of bacterial community structure. C3 plants exhibited higher abundances of Proteobacteria, Bacteroidetes at the phylum level and Sphingomicrobium at the genus level, compared to C4 plants. Conversely, C4 plants had higher abundances of Actinobacteria and Patescibacteria at the phylum level and Nocardioides at the genus level. LEfSe and function prediction analyses revealed that the rhizosphere soil bacteria in C3 plants exhibited significantly higher enrichment in nitrogen fixation functions (p < 0.05), whereas C4 plants showed a significantly higher relative abundance of bacteria and functions related to organic pollutant degradation (p < 0.05). These findings suggest that the rhizosphere soil bacteria of C3 plants exhibit a stronger response to BTBPE exposure in nitrogen metabolism-related processes, while C4 plants possess superior biodegradation ability compared to C3 plants.

Green manure (Ophiopogon japonicus) cover promotes tea plant growth by regulating soil carbon cycling.

In mountainous tea plantations, which are the primary mode of tea cultivation in China, issues such as soil erosion and declining soil fertility are particularly severe. Although green manure cover is an effective agricultural measure for restoring soil fertility, its application in mountainous tea plantations has been relatively understudied. This study investigated the effects of continuous green manure cover using the slope-protecting plant Ophiopogon japonicus on tea plant growth and soil microbial community structure. We implemented three treatments: 1 year of green manure coverage, 2 years of coverage, and a control, to study their effects on tea plant growth, soil physicochemical properties, and soil bacterial and fungal communities. Results demonstrate that green manure coverage significantly promote the growth of tea plants, enhanced organic matter and pH levels in soil, and various enzyme activities, including peroxidases and cellulases. Further functional prediction results indicate that green manure coverage markedly promoted several carbon cycling functions in soil microbes, including xylanolysis, cellulolysis, degradation of aromatic compounds, and saprotrophic processes. LEfSe analysis indicated that under green manure cover, the soil tends to enrich more beneficial microbial communities with degradation functions, such as Sphingomonas, Sinomonas, and Haliangium (bacteria), and Penicillium, Apiotrichum, and Talaromyce (fungi). In addition. Random forest and structural equation models indicated that carbon cycling, as a significant differentiating factor, has a significant promoting effect on tea plant growth. In the management practices of mountainous tea plantations, further utilizing slope-protecting plants as green manure can significantly influence the soil microbial community structure and function, enriching microbes involved in the degradation of organic matter and aromatic compounds, thereby positively impacting tea tree growth and soil nutrient levels.

Potential applications of microbial genomics in nuclear non-proliferation.

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as "characteristic communities of microorganisms" found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

Mode of application of sulfonated graphene modulated bioavailable heavy metal contents and microbial community composition in long-term heavy metal contaminated soil

Nanomaterials are increasingly recognized for their potential in soil remediation. However, their impact on soil microbial communities in contaminated soil remains poorly understood. In this study, we investigated the dynamic effects of sulfonated graphene (SG) following one-time or repeated applications on heavy metal availability and soil microbial communities in long-term heavy metal-contaminated soil over 180 days. Our findings revealed that one-time SG application at 30 mg kg−1 significantly increased the bioavailable cadmium (Cd) and copper (Cu) contents by approximately 30 %–40 % after 2 and 180 days. Repeated SG applications, however, displayed no significant influence on heavy metal availability. One-time SG application, coupled with the increased available Cd, induced significant enrichment of some specific functional bacterial genera involved in glycan biosynthesis metabolism and biosynthesis of other secondary metabolites, thereby decreasing the available contents of heavy metals after 90 days. However, the shifts in bacterial community structure and function were subsequently partially recovered after 180 days. Conversely, repeated SG treatments led to minimal alterations after 90 days while leading to similar shifts in the bacterial community at 60 mg kg−1 after 180 days. The fungal community structure remained largely unaltered across all SG treatments. Intriguingly, SG treatments substantially stimulated fungal biomass, with the stimulation degree dependent on SG dosage. These results provide valuable insights for developing phytoremediation strategies, suggesting tailored SG applications during specific growth phases to optimize remediation efficiency.

Direct and indirect effects of copepod grazers on community structure

Abstract Ecological theory and empirical research show that both direct lethal effects and indirect non-lethal effects can structure the composition of communities. While the direct effects of grazers on marine phytoplankton communities are well studied, their indirect effects are still poorly understood. Direct and indirect effects are inherently difficult to disentangle in plankton food webs. In this study we evaluate the indirect effects of copepod grazers on community function and structure using isolated chemical alarm signals, copepodamides. We expose intact summer and spring communities to direct grazing from copepods, or to chemical alarm cues without the presence of grazers in controlled experiments. The effects of direct grazing on ecosystem function were moderate in both experiments as indicated by levels of chlorophyll and primary production. Indirect and direct effects resulted in changes in the composition of both the eukaryote and prokaryote communities as shown by metabarcoding of 18S and 16S rRNA. Size structure analysis suggests that direct grazing and copepodamide exposure both favoured smaller organisms (< 10–15 μm) corroborating the size-structuring effect of copepod grazers. We conclude that the well-established effect of copepods on phytoplankton communities results from a combination of direct and indirect effects. This is a first attempt to isolate indirect effects of copepods on community structure and the results suggest that a full mechanistic understanding of the structuring effect of copepods will require insights to both direct and indirect effects of consumers as demonstrated for other ecosystems components.

Parasites disrupt a keystone mutualism that underpins the structure, functioning, and resilience of a coastal ecosystem

AbstractParasites can alter the traits or densities of mutualistic partners, potentially destabilizing mutualistic associations that underpin the structure, functioning, and stability of entire ecosystems. Despite the potentially wide‐ranging consequences of such disruptions, no studies have directly manipulated parasite prevalence and/or intensity in a mutualistic partner, nor quantified the resulting community‐level effects. Here, we investigated the effects of a common trematode parasite (Cercaria opaca) on the strength of a keystone facultative mutualism in western Atlantic salt marshes between the foundational marsh cordgrass, Spartina alterniflora, and the ribbed mussel, Geukensia demissa. Cordgrass increases mussel survivorship and growth through shading, while mussels enhance cordgrass growth by producing nutrient‐rich biodeposits. This mutualistic association also creates conditions that enhance biodiversity and ecosystem functioning, and mediates the ability of foundational plants to resist and recover from extreme drought. We used lab and field assays to show how increasing infection with trematode metacercariae negatively influenced mussel biodeposit production, as well as the strength of mussel shells and byssal attachments. By conducting a field manipulation using experimentally infected mussels, we demonstrated that the mutualistic benefits of mussels to cordgrass growth decreased with increasing trematode infection intensity—a pattern likely generated by reduced mussel biodeposition and enhanced mortality. Additionally, increasing parasite loads in mussels led to predictable decreases in the abundances of benthic invertebrates, as well as in key ecosystem characteristics and process rates (i.e., redox potential and sediment accretion). Finally, a survey of five North Carolina salt marshes demonstrated that infection with C. opaca was most common in mussels in areas experiencing cordgrass die‐off due to drought, and that infection intensity decreased with distance from die‐off areas. Because the mussel–cordgrass mutualism underpins marsh ecosystem resilience to drought‐associated die‐off, our results suggest that parasitism may depress recovery from these disturbances. Although this is the first experimental demonstration of parasites indirectly altering community structure and functioning by undermining an ecologically influential mutualism, this type of relationship could be common in nature, given that parasites frequently infect influential mutualists.

Removal of enrofloxacin as well as nutrients in mariculture water by Sesuvium portulacastrum system: Insights for biodegradation, ecotoxicity of enrofloxacin

Antibiotic contamination and eutrophication in mariculture have become problems that cannot be ignored, and enrofloxacin (ENR), as an example, is especially widely used in mariculture. This study firstly revealed that Sesuvium portulacastrum, a plant with world-wide distribution in coastal zones, with its rhizosphere microorganisms, could remove ENR as well as nutrients. The S. portulacastrum system could degrade ENR to small-molecule products 1,2,3,4-tetrahydroquinolin-4-ol and (2,4-dihydroxyphenyl)-cyclopropylamine. And there were 81.3–39.2 % removals of ENR with 0.01-100 mg/L. Although ENR significantly influenced functions of rhizosphere microbial community, like decreasing nitrogen fixation, shifting trophic strategies from phototrophy to chemoheterotrophy, nutrients (NH4+-N, NO2−-N, NO3−-N and total dissolved phosphorus) removal of S. portulacastrum system was essentially unaffected at low ENR concentration (< 1 mg/L). The removal mechanism of S. portulacastrum system was explored. Neither of the isolated root exudates and rhizosphere bacteria could degrade ENR, however, without rhizosphere bacteria, ENR removal rate would decrease. Root proteins including oxidase, decarboxylase, dehydrogenase, such as laccase, isocitrate dehydrogenase, delta-1-pyrroline-5-carboxylate dehydrogenase were overexpressed. Additionally, endocytosis is a pathway for antibiotics to enter S. portulacastrum. This study demonstrated that S. portulacastrum system could be used for remediation of antibiotics-nutrients combined pollution, and deepened understanding the antibiotic removal mechanism of macrophytes in mariculture, moreover, provided new macroplant species and a theoretical basis for antibiotics removal in aquatic systems.

Characteristics of Bacterial Community Structure and Function in Artificial Soil Prepared Using Red Mud and Phosphogypsum.

The preparation of artificial soil is a potential cooperative resource utilization scheme for red mud and phosphogypsum on a large scale, with a low cost and simple operation. The characteristics of the bacterial community structure and function in three artificial soils were systematically studied for the first time. Relatively rich bacterial communities were formed in the artificial soils, with relatively high abundances of bacterial phyla (e.g., Cyanobacteria, Proteobacteria, Actinobacteriota, and Chloroflexi) and bacterial genera (e.g., Microcoleus_PCC-7113, Rheinheimera, and Egicoccus), which can play key roles in various nutrient transformations, resistance to saline-alkali stress and pollutant toxicity, the enhancement of various soil enzyme activities, and the ecosystem construction of artificial soil. There were diverse bacterial functions (e.g., photoautotrophy, chemoheterotrophy, aromatic compound degradation, fermentation, nitrate reduction, cellulolysis, nitrogen fixation, etc.), indicating the possibility of various bacteria-dominated biochemical reactions in the artificial soil, which can significantly enrich the nutrient cycling and energy flow and enhance the fertility of the artificial soil and the activity of the soil life. The bacterial communities in the different artificial soils were generally correlated with major physicochemical factors (e.g., pH, OM, TN, AN, and AP), as well as enzyme activity factors (e.g., S-UE, S-SC, S-AKP, S-CAT, and S-AP), which comprehensively illustrates the complexity of the interaction between bacterial communities and environmental factors in artificial soils, and which may affect the succession direction of bacterial communities, the quality of the artificial soil environment, and the speed and direction of the development and maturity of the artificial soil. This study provides an important scientific basis for the synergistic soilization of two typical industrial solid wastes, red mud and phosphogypsum, specifically for the microbial mechanism, for the further evolution and development of artificial soil prepared using red mud and phosphogypsum.

Effects of long-term continuous cultivation on the structure and function of soil bacterial and fungal communities of Fritillaria Cirrhosa on the Qinghai-Tibetan Plateau.

Fritillaria cirrhosa, an endangered medicinal plant in the Qinghai-Tibet Plateau, is facing resource scarcity. Artificial cultivation has been employed to address this issue, but problems related to continuous cultivation hinder successful transplantation. Imbalanced microbial communities are considered a potential cause, yet the overall changes in the microbial community under continuous cropping systems remain poorly understood. Here, we investigated the effects of varying durations of continuous cropping on the bacterial and fungal communities, as well as enzymatic activities, in the rhizospheric soil of F. cirrhosa. Our findings revealed that continuous cropping of F. cirrhosa resulted in soil acidification, nutrient imbalances, and increased enzyme activity. Specifically, after 10 years of continuous cropping, there was a notable shift in the abundance and diversity (e.g., Chao1 index) of soil bacteria and fungi. Moreover, microbial composition analyses revealed a significant accumulation of harmful microorganisms associated with soil-borne diseases (e.g., Luteimonas, Parastagonospora, Pseudogymnoascus) in successively cropped soils, in contrast to the significant reduction of beneficial microorganisms (e.g., Sphingomonas, Lysobacter, Cladosporium) that promote plant growth and development and protect against diseases such as Fusarium sp.These changes led to decreased connectivity and stability within the soil microbial community. Structural equation modeling and redundancy analysis revealed that alkaline hydrolytic nitrogen and available phosphorus directly influenced soil pH, which was identified as the primary driver of soil microbial community changes and subsequently contributed to soil health deterioration. Overall, our results highlight that soil acidification and imbalanced rhizosphere microbial communities are the primary challenges associated with continuous cropping of F. cirrhosa. These findings establish a theoretical foundation for standardized cultivation practices of F. cirrhosa and the bioremediation of continuously cultivated soils.

Invasive Amaranthus spp. for heavy metal phytoremediation: Investigations of cadmium and lead accumulation and soil microbial community in three zinc mining areas

Amaranthus spp. are a group of strongly invasive and vigorous plants, and heavy metal phytoremediation using alien invasive Amaranthus spp. has been a popular research topic. In this study, the bioconcentration factor (BCF) and translocation factor (TF) of Amaranthus spp. were evaluated, focusing on the accumulation potential of cadmium (Cd) and lead (Pb) by plants from three different zinc mining areas, namely Huayuan (HYX), Yueyang (LYX), and Liuyang (LYX). The HYX area has the most severe Cd contamination, while the LYX area has the most apparent Pb contamination. The results showed that Amaranthus spp. had a strong Cd and Pb enrichment capacity in low-polluted areas. To elucidate the underlying mechanisms, we used high-throughput sequencing of 16S rRNA and internal transcribed spacer (ITS) regions to analyze rhizosphere bacterial and fungal communities in three areas. The results showed significant differences in the structure, function, and composition of microbial communities and complex interactions between plants and their microbes. The correlation analysis revealed that some key microorganisms (e.g., Amycolatopsis, Bryobacterium, Sphingomonas, Flavobacterium, Agaricus, Nigrospora, Humicola) could regulate several soil factors such as soil pH, organic matter (OM), available nitrogen (AN), and available phosphorus (AP) to affect the heavy metal enrichment capacity of plants. Notably, some enzymes (e.g., P-type ATPases, Cysteine synthase, Catalase, Acid phosphatase) and genes (e.g., ZIP gene family, and ArsR, MerR, Fur, NikR transcription regulators) have been found to be involved in promoting Cd and Pb accumulation in Amaranthus spp. This study can provide new ideas for managing heavy metal-contaminated soils and new ways for the ecological resource utilization of invasive plants in phytoremediation.

Intercropping with Robinia pseudoacacia reduces soft rot incidence in konjac by modulating the root bacterial community.

Soft rot (Pectobacterium aroidearum and Dickeya) is a devastating soil-borne bacterial disease that threatens konjac production. Intercropping with false acacia has been shown to significantly reduce soft rot incidence in konjac by shifting the microbial community. However, how intercropping shapes the root bacterial community and affects soft rot incidence remains unclear. To address this, we investigated three konjac intercropping systems (false acacia, paulownia, and maize) to explore the relationships among intercropping, soft rot incidence, root bacterial community, soil enzyme activity, and soil properties. Konjac intercropped with false acacia exhibited the lowest soft rot incidence and the lowest abundance of pathogenic taxa. Soft rot incidence was negatively correlated with total soil nitrogen and potassium but positively correlated with total and available soil phosphorus. The bacterial community structure and function in konjac roots differed among intercropping types, mainly driven by available soil phosphorus. Beneficial microorganisms such as Bradyrhizobium and Variovorax were enriched under a false acacia intercropping system and were negatively correlated with soil-available phosphorus. Additionally, the stable bacterial community in healthy konjac roots under false acacia may make konjac less susceptible to pathogen invasion. The study showed that intercropping reduced the soft rot incidence by regulating the structure and stability of the konjac root bacterial community, and soil-available phosphorus was the main factor affecting the difference in the konjac root bacterial community, which provided a basis for the management of soil fertilization in konjac cultivation. © 2024 Society of Chemical Industry.

Investigating Changes in the Soil Fungal Community Structure, Functions, and Network Stability with Prolonged Grafted Watermelon Cultivation

Investigating Changes in the Soil Fungal Community Structure, Functions, and Network Stability with Prolonged Grafted Watermelon Cultivation

Minimum area of primitive broad-leaved Korean pine forest community based on biomass

Based on the survey data of nine primitive broad-leaved Korean pine forest plots ranging from 1 to 10.4 ha in Heilongjiang Province, this study used the moving window method and GIS technology to analyze the variation characteristics of the spatial distribution pattern of forest biomass in each plot. We explored the minimum area that can reflect the structural and functional characteristics of the primitive broad-leaved Korean pine forest, and used computer simulation random sampling method to verify the accuracy of the minimum area. The results showed that: (1) Through the analysis of the spatial distribution raster map of biomass deviation in the plots at various scales of 10 − 100 m, there is a minimum area (0.64 ha) for the critical range of biomass density variation in the primitive broad-leaved Korean pine forest. This minimum area based on biomass density can indirectly reflect the comprehensive characteristics of productivity level per unit area, structure, function, and environmental quality of the primitive broad-leaved Korean pine forest community. (2) Using computer simulation random sampling, it was found that only by sampling in a specific plot larger than or equal to the minimum area can equivalent or similar results be achieved as random sampling within the plot, indicating that the minimum area determined by the moving window method is accurate. (3) The minimum area determined in this paper is an excellent indicator reflecting the complexity of community structure, which can be used for comparing changes in community structure and function before and after external disturbances, and has a good evaluation effect. This minimum area can also be used as a basis for scientific and reasonable setting of plot size in the investigation and monitoring work of broad-leaved Korean pine forests in this region, thereby achieving the goals of improving work efficiency and saving work costs.

Metagenomic analysis of soil from landfill site reveals a diverse microbial community involved in plastic degradation

In this study, we have investigated microbial communities structure and function using high throughput amplicon sequencing and whole metagenomic sequencing of DNA extracted from different depths of a plastic-laden landfill site. With diverse taxonomic groups inhabiting the plastic-rich soil, our study demonstrates the remarkable adaptability of microbes to use this new substrate as a carbon source. FTIR spectroscopic analysis of soil indicated degradation of plastic as perceived from the carbonyl index of 0.16, 0.72, and 0.44 at 0.6, 0.9 and 1.2 m depth, respectively. Similarly, water contact angles of 108.7 degree, 99.7 degree, 62.7 degree, and 77.8 degree of plastic pieces collected at 0.3, 0.6, 0.9, and 1.2 m depths respectively showed increased wettability and hydrophilicity of the plastic. Amplicon analysis of 16S and 18 S rRNA revealed a high abundance of several plastic-degrading bacterial groups, including Pseudomonas, Rhizobiales, Micrococcaceae, Chaetomium, Methylocaldum, Micromonosporaceae, Rhodothermaceae and fungi, including Trichoderma, Aspergillus, Candida at 0.9 m. The co-existence of specific microbial groups at different depths of landfill site indicates importance of bacterial and fungal interactions for plastic. Whole metagenome analysis of soil sample at 0.9 m depth revealed a high abundance of genes encoding enzymes that participate in the biodegradation of PVC, polyethylene, PET, and polyurethane. Curation of the pathways related to the degradation of these materials provided a blueprint for plastic biodegradation in this ecosystem. Altogether, our study has highlighted the importance of microbial cooperation for the biodegradation of pollutants. Our metagenome-based investigation supports the current perception that consortia of fungi-bacteria are preferable to axenic cultures for effective bioremediation of the environment.

Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes.

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.

The influence of urban environmental effects on the orchard soil microbial community structure and function: a case study in Zhejiang, China.

The urban environmental effects can have multifaceted impacts on the orchard soil microbial community structure and function. To specifically study these effects, we investigated the soil bacterial and fungal community in the laxly managed citrus orchards using amplicon sequencing. Ascomycota demonstrated significant dominance within the citrus orchard soils. The increased presence of beneficial Trichoderma spp. (0.3%) could help suppress plant pathogens, while the elevated abundance of potential pathogenic fungi, such as Fusarium spp. (0.4%), might raise the likelihood of disorders like root rot, thereby hindering plant growth and resulting in reduced yield. Moreover, we observed significant differences in the alpha and beta diversity of bacterial communities between urban and rural soils (p < 0.001). Environmental surveys and functional prediction of bacterial communities suggested that urban transportation factors and rural waste pollution were likely contributing to these disparities. When comparing bacterial species in urban and rural soils, Bacillus spp. exhibited notable increases in urban areas. Bacillus spp. possess heavy metal tolerance attributed to the presence of chromium reductase and nitroreductase enzymes involved in the chromium (VI) reduction pathway. Our findings have shed light on the intricate interplay of urban environmental effects and root systems, both of which exert influence on the soil microbiota. Apart from the removal of specific pollutants, the application of Bacillus spp. to alleviate traffic pollution, and the use of Trichoderma spp. for plant pathogen suppression were considered viable solutions. The knowledge acquired from this study can be employed to optimize agricultural practices, augment citrus productivity, and foster sustainable agriculture.

The effect of combinations of a glyphosate-based herbicide with various clinically used antibiotics on phenotypic traits of Gram-negative species from the ESKAPEE group

The emission of glyphosate and antibiotic residues from human activities threatens the diversity and functioning of the microbial community. This study examines the impact of a glyphosate-based herbicide (GBH) and common antibiotics on Gram-negative bacteria within the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli). Ten strains, including type and multidrug-resistant strains for each species were analysed and eight antibiotics (cefotaxime, meropenem, aztreonam, ciprofloxacin, gentamicin, tigecycline, sulfamethoxazole-trimethoprim, and colistin) were combined with the GBH. While most combinations yielded additive or indifferent effects in 70 associations, antagonistic effects were observed with ciprofloxacin and gentamicin in five strains. GBH notably decreased the minimum inhibitory concentration of colistin in eight strains and displayed synergistic activity with meropenem against metallo-β-lactamase (MBL)-producing strains. Investigation into the effect of GBH properties on outer membrane permeability involved exposing strains to a combination of this GBH and vancomycin. Results indicated that GBH rendered strains sensitive to vancomycin, which is typically ineffective against Gram-negative bacteria. Furthermore, we examined the impact of GBH in combination with three carbapenem agents on 14 strains exhibiting varying carbapenem-resistance mechanisms to assess its effect on carbapenemase activity. The GBH efficiently inhibited MBL activity, demonstrating similar effects to EDTA (ethylenediaminetetraacetic acid). Chelating effect of GBH may have multifaceted impacts on bacterial cells, potentially by increasing outer membrane permeability and inactivating metalloenzyme activity.

Responses of soil fungal community composition and function to wetland degradation in the Songnen Plain, northeastern China.

Wetlands are ecosystems that have a significant impact on ecological services and are essential for the environment. With the impacts of rapid population growth, wetland reclamation, urbanization, and land use change, wetlands have undergo severe degradation or loss. However, the response of soil fungal communities to wetland degradation remains unknown. It is crucial to comprehend how the diversity and population dynamics of soil fungi respond to varying levels of degradation and ecological progression in the wetlands of the Songnen Plain. In this study, high- throughput sequencing technology to analyze the variety and abundance of soil fungi in the undegraded (UD), light degraded (LD), moderate degraded (MD), and severe degraded (SD) conditions in the Halahai Nature Reserve of Songnen Plain. This study also explored how these fungi are related to the soil's physicochemical properties in wetlands at various degradation levels. The findings indicated that Basidiomycota and Ascomycota were the primary phyla in the Songnen Plain, with Ascomycota increasing and Basidiomycota decreasing as wetland degradation progressed. Significant differences were observed in soil organic carbon (SOC), total nitrogen (TN),and soil total potassium (TK) among the succession degradation stages. With the deterioration of the wetland, there was a pattern of the Shannon and Chao1 indices increasing and then decreasing. Non-metric Multidimensional Scaling (NMDS) analysis indicated that the fungal community structures of UD and LD were quite similar, whereas MD and SD exhibited more distinct differences in their fungal community compositions. Redundancy analysis (RDA) results indicated that Soil Water content (SWC) and total nitrogen (TN) were the primary environmental factors influencing the dominant fungal phylum. According to the FUNGuild prediction, Ectomycorrhizal and plant pathogens gradually declining with wetland degradation. In general, our findings can offer theoretical support develop effective solutions for the preservation and rehabilitation of damaged wetlands.