The influence of elevated CO2 on bacterial community structure and its co-occurrence network in soils polluted with Cr2O3 nanoparticles

Elevated CO2 alters antibiotic resistome in soil amended with sulfamethazine via chemical-organic fertilization

Rising antimicrobial resistance (AMR) is an enormous challenge for global healthcare systems. The effects of elevated CO2 (eCO2) on AMR are poorly characterized. Using a free-air CO2 enrichment system and high-throughput qPCR arrays, we investigated the response of soil antibiotic resistome and bacterial communities to eCO2 (ambient + 200 ppm) in soils amended with sulfamethazine (SMZ) at 0.1 and 1 mg kg-1 via chemical-organic fertilizer (COL, COH). Results showed that under ambient condition, COH significantly enhanced the diversity of high-risk antibiotic resistance genes (ARGs), relative abundance of low risk ARGs, unassessed ARGs and total ARGs compared to COL. Nevertheless, eCO2 mitigated the effects of COH, with no significant difference found between COL and COH on the above high risk, low risk, unassessed and total ARGs. Meanwhile, eCO2 decreased the relative abundance of spcN, ermA, olec, oprD, sulA-olP, tetB, tetT and vanXD in COL, and alleviated the enrichment of pikR2, ampC, lunC, oprD and pncA caused by the application of SMZ at 1 mg kg-1. Correlation and network analysis illustrated that changes of certain bacteria biomarkers and horizontal gene transfer of integrase gene were associated with the altered response of ARGs abundance to eCO2. This study adds knowledge of the potential risk of antibiotic resistance in agricultural exposure scenarios under increasing CO2 concentration.

Land use modified impacts of global change factors on soil microbial structure and function: A global hierarchical meta-analysis

Nitrogen cycling in terrestrial ecosystems is critical for biodiversity, vegetation productivity and biogeochemical cycling. However, little is known about the response of functional nitrogen cycle genes to global change factors in soils under different land uses. Here, we conducted a multiple hierarchical mixed effects meta-analyses of global change factors (GCFs) including warming (W+), mean altered precipitation (MAP+/-), elevated carbon dioxide concentrations (eCO2), and nitrogen addition (N+), using 2706 observations extracted from 200 peer-reviewed publications. The results showed that GCFs had significant and different effects on soil microbial communities under different types of land use. Under different land use types, such as Wetland, Tundra, Grassland, Forest, Desert and Agriculture, the richness and diversity of soil microbial communities will change accordingly due to differences in vegetation cover, soil management practices and environmental conditions. Notably, soil bacterial diversity is positively correlated with richness, but soil fungal diversity is negatively correlated with richness, when differences are driven by GCFs. For functional genes involved in nitrification, eCO2 in agricultural soils and the interaction of N+ with other GCFs in grassland soils stimulate an increase in the abundance of the AOA-amoA gene. In agricultural soil, MAP+ increases the abundance of nifH. W+ in agricultural soils and N+ in grassland soils decreased the abundance of nifH. The abundance of the genes nirS and nirK, involved in denitrification, was mainly negatively affected by W+ and positively affected by eCO2 in agricultural soil, but negatively affected by N+ in grassland soil. This meta-analysis was important for subsequent research related to global climate change. Considering data limitations, it is recommended to conduct multiple long-term integrated observational experiments to establish a scientific basis for addressing global changes in this context.

Biochar impacts on carbon dioxide, methane emission, and cadmium accumulation in rice from Cd-contaminated soils; A meta-analysis

Climate change and cadmium (Cd) contamination pose severe threats to rice production and food security. Biochar (BC) has emerged as a promising soil amendment for mitigating these challenges. To investigate the BC effects on paddy soil upon GHG emissions, Cd bioavailability, and its accumulation, a meta-analysis of published data from 2000 to 2023 was performed. Data Manager 5.3 and GetData plot Digitizer software were used to obtain and process the data for selected parameters. Our results showed a significant increase of 18% in soil pH with sewage sludge BC application, while 9% increase in soil organic carbon (SOC) using bamboo chips BC. There was a significant reduction in soil bulk density (8%), but no significant effects were observed for soil porosity, except for wheat straw BC which reduced the soil porosity by 6%. Sewage sludge and bamboo chips BC significantly reduced carbon dioxide (CO2) by 7-8% while municipal biowaste reduced methane (CH4) emissions by 2%. In the case of heavy metals, sunflower seedshells-derived materials and rice husk BC significantly reduced the bioavailable Cd in paddy soils by 24% and 12%, respectively. Cd uptake by rice roots was lowered considerably by the addition of kitchen waste (22%), peanut hulls (21%), and corn cob (15%) based BC. Similarly, cotton sticks, kitchen waste, peanut hulls, and rice husk BC restricted Cd translocation from rice roots to shoots by 22%, 27%, 20%, and 19%, respectively, while sawdust and rice husk-based BC were effective for reducing Cd accumulation in rice grains by 25% and 13%. Regarding rice yield, cotton sticks-based BC significantly increased the yield by 37% in Cd-contaminated paddy soil. The meta-analysis demonstrated that BC is an effective and multi-pronged strategy for sustainable and resilient rice cultivation by lowering greenhouse gas emissions and Cd accumulation while improving yields under the increasing threat of climate change.

Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.

Mammalian carcass decay increases carbon storage and temporal turnover of carbon-fixing microbes in alpine meadow soil

Corpse decomposition is of great significance to the carbon cycle of natural ecosystem. Carbon fixation is a carbon conversion process that converts carbon dioxide into organic carbon, which greatly contributes to carbon emission reduction. However, the effects of wild animal carcass decay on carbon-fixing microbes in grassland soil environment are still unknown. In this research, thirty wild mammal (Ochotona curzoniae) corpses were placed on alpine meadow soil to study the carbon storage and carbon-fixing microbiota succession for a 94-day decomposition using next-generation sequencing. Our results revealed that 1) the concentration of total carbon increased approximately 2.24-11.22% in the corpse group. 2) Several carbon-fixing bacterial species (Calothrix parietina, Ancylobacter rudongensis, Rhodopseudomonas palustris) may predict the concentration of total carbon. 3) Animal cadaver degradation caused the differentiation of carbon-fixing microbiota structures during succession and made the medium-stage networks of carbon-fixing microbes more complicated. 4) The temporal turnover rate in the experimental groups was higher than that in the control groups, indicating a quick change of gravesoil carbon-fixing microbiota. 5) The deterministic process dominates the assembly mechanism of experimental groups (ranging from 53.42% to 94.94%), which reflects that the carbon-fixing microbial community in gravesoil can be regulated. Under global climate change, this study provides a new perspective for understanding the effects of wild animal carcass decay on soil carbon storage and carbon-fixing microbes.

Recent Advances and Perspectives of Nanomaterials in Agricultural Management and Associated Environmental Risk: A Review

The advancement in nanotechnology has enabled a significant expansion in agricultural production. Agri-nanotechnology is an emerging discipline where nanotechnological methods provide diverse nanomaterials (NMs) such as nanopesticides, nanoherbicides, nanofertilizers and different nanoforms of agrochemicals for agricultural management. Applications of nanofabricated products can potentially improve the shelf life, stability, bioavailability, safety and environmental sustainability of active ingredients for sustained release. Nanoscale modification of bulk or surface properties bears tremendous potential for effective enhancement of agricultural productivity. As NMs improve the tolerance mechanisms of the plants under stressful conditions, they are considered as effective and promising tools to overcome the constraints in sustainable agricultural production. For their exceptional qualities and usages, nano-enabled products are developed and enforced, along with agriculture, in diverse sectors. The rampant usage of NMs increases their release into the environment. Once incorporated into the environment, NMs may threaten the stability and function of biological systems. Nanotechnology is a newly emerging technology, so the evaluation of the associated environmental risk is pivotal. This review emphasizes the current approach to NMs synthesis, their application in agriculture, interaction with plant-soil microbes and environmental challenges to address future applications in maintaining a sustainable environment.

Soil microbiome feedback to climate change and options for mitigation

Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resultant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO₂ and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to generalize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodological choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as genetically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.

Simplifying network complexity of soil bacterial community exposed to short-term carbon dioxide and ozone enrichment in a paddy soil

Global atmospheric changes are characterized by increases in carbon dioxide (CO₂) and ozone (O₃) concentrations, with important consequences for the soil microbial community. However, the influences of CO₂ and O₃ enrichment on the biomass, diversity, composition, and functioning of the soil bacterial community remain unclear. We investigated the effects of short-term factorial combinations of CO₂ (by 200 ppm) and O₃ (by 40 ppb) enrichment on the dynamics of soil bacterial community in paddy soils with two rice varieties (Japonica, Nangeng 5055 (NG5055) vs. Wuyujing 3 (WYJ3)) in an open top chamber facility. When averaged both varieties, CO₂ and O₃ enrichment showed no individual or combined effect on the abundance or diversity of soil bacterial community. Similarly, CO₂ enrichment did not exert any significant effect on the relative abundance of bacterial phyla. However, O₃ enrichment significantly reduced the relative abundance of Myxococcota phylum by a mean of 37.5%, which negatively correlated to root N content. Compared to ambient conditions, soil bacterial community composition was separated by CO₂ enrichment in NG5055, and by both CO₂ and O₃ enrichment in WYJ3, with root N content identified as the most influential factor. These results indicated that root N was the top direct predictor for the community composition of soil bacteria. The COG (cluster of orthologous groups) protein of cell motility was significantly reduced by 5.8% under CO₂ enrichment, and the COG protein of cytoskeleton was significantly decreased by 14.7% under O₃ enrichment. Furthermore, the co-occurrence network analysis indicated that both CO₂ and O₃ enrichment decreased the network complexity of the soil bacterial community. Overall, our results highlight that continuous CO₂ and O₃ enrichment would potentially damage the health of paddy soils through adverse impacts on the associations and functional composition of soil microbial communities.

The effects of g-C3N4/biochar and g-C3N4 on bacterial community in riverbed sediment

Biochar had been widely used to improve the activity of photocatalysts, the biochar-based photocatalysts had more potential for environmental pollution remediation, but their effect on the sediment remained unknown. To understand these, the typical photocatalyst g-C₃N₄ was modified by biochar to develop g-C₃N₄/biochar with enhanced photocatalytic ability. Riverbed sediment was exposed to g-C₃N₄ and g-C₃N₄/biochar respectively for 30 days, and Illumina sequencing was utilized to examine the changes in the bacterial community in the sediment. The results showed that in riverbed sediment, g-C₃N₄ exposure had a concentration-dependent effect on the diversity of bacteria, while g-C₃N₄/biochar exposure had a slight influence on the bacterial diversity and the diversity almost maintained stable with different g-C₃N₄/biochar concentration. The application of g-C₃N₄ exhibited an inhibition influence on the growth of Acidobacteria, Gemmatimonadetes, and Rokubacteria in sediment, whose relative abundance increased when g-C₃N₄ was 25 mg/kg, and then decreased when g-C₃N₄ beyond this concentration. The presence of g-C₃N₄/biochar increased the relative abundance of Cyanobacteria in sediment and showed no obvious impact on other dominant phyla. Both g-C₃N₄ and g-C₃N₄/biochar could alter the levels of TP, NN, and AN in the sediment, but the magnitude of the changes of these physicochemical factors caused by g-C₃N₄/biochar was much smaller than those caused by g-C₃N₄. In addition, the complexity of the bacterial community network was reduced in a high concentration of g-C₃N₄, while it remained stable with different concentrations of g-C₃N₄/biochar treatments. Totally, this study demonstrated that, compared to g-C₃N₄, g-C₃N₄/biochar was able to maintain the relative stability of the bacterial community in riverbed sediment and mitigate the negative effects of photocatalysts to some extent, making biochar an ecological remediation agent with great potential for application.

Characteristics of soil carbon emissions and bacterial community composition in peatlands at different stages of vegetation succession

Microorganisms are important components of soil ecosystems and play an important role in material cycles. Northern peatlands are important ecosystems in middle-high latitude regions. In peatlands, different vegetation successions occur with changes in groundwater levels. The overall carbon emission of peat bogs is related to the carbon stability of the surrounding environment. Unraveling the assembly and distribution of bacterial communities at different succession stages in peatland is essential to understanding the soil nutrient cycle. In this study, we investigated the characteristics of soil carbon emissions and the composition of subsurface microorganisms under six different succession stages. The highest carbon emission was observed in mossy peatlands, and their soil enzyme activity was closely related to the aboveground vegetation cover type. The succession pattern of ground vegetation was the main driver of soil microorganisms. The abundance of the dominant Proteobacteria decreased with increasing soil depth, while the opposite trend was observed for Chloroflexi. Furthermore, the community structure of microorganisms became progressively simpler and looser as soil water content decreased. The bacterial alpha diversity was driven by soil dissolved organic carbon and Fe, and the beta diversity was driven mainly by soil water content. The bacteria presented a random distribution in a nutrient-rich soil environment and shifted to deterministic distribution with decreasing water and nutrient contents. The balance between taxonomic diversity and dispersal limitation mediates species coexistence in the soil microbiome. This study provides new insights into the soil environment at different stages of succession in peatlands.

Effects of anthropogenic nitrogen additions and elevated CO2 on microbial community, carbon and nitrogen content in a replicated wetland

Anthropogenic deposition of nitrogen (N) and elevated CO₂ (_eaCO₂) are expected to increase continuously and rapidly in the near future and influence global carbon cycling. These parameters affect the ecosystem by regulating the microbial community and contribute to soil organic matter decomposition. The study was performed to understand the effects of N additions (4 and 6mgl^-1) and _eaCO₂ (700 ppm) on carbon (C)/nitrogen (N) content in the soil, microbial community, and plant biomass (Alternanthera philoxeroides species). The results showed that when the atmospheric CO₂ concentration was raised, the total organic carbon (TOC) in the soil statistically increased (P < 0.05) by 4% and 3% under low and high N additions respectively, while the inorganic carbon content also increased by 1% and 3% (P > 0.05) under the same conditions. The increase in the soil TOC content was a result of the movement of carbon from water to the soil due to the presence of vascular tissues of plants in the water. The redundancy analysis (RDA) results revealed that the presence of plant species was responsible for the carbon content increment in the soil. The plant biomass content increased by 30.96% (P = 0.081) and 31.36%, (P = 0.002) under low and high N addition respectively due to the increment in atmospheric CO₂. The nitrogen content in the plant species decreased (p > 0.05) by 8.62% and 6.25% at low and high N addition respectively when atmospheric CO₂ was raised. This suggests that soil microbes competed with the plants for inorganic nitrogen in the soil and the microbes used up the inorganic nitrogen before it got to the plants. The gram-positive bacteria and fungi population decreased under high N addition and _eaCO₂ while gram-negative bacteria increased, suggesting that N additions and _eaCO₂ affected the microbial function and correlated with the nitrogen reduction in the soil. The results from this study serve as a guide to researchers and stakeholders in making policies with regard to the constant increasing CO₂ concentration in the atmosphere.

Soil Type Influences Rhizosphere Bacterial Community Assemblies of Pecan Plantations, a Case Study of Eastern China

The rhizosphere microbiome is closely related to forest health and productivity. However, whether soil type affects pecan (Carya illinoinensis) rhizosphere microbiomes is unclear. We aimed to explore the diversity and structural characteristics of rhizosphere bacteria associated with pecan plantations grown in three soil types (Luvisols, Cambisols, Solonchaks) in Eastern China and analyze their potential functions through high-throughput sequencing. The results showed that the diversity and community structure of rhizosphere bacteria in pecan plantations were significantly affected by soil type and the pH, available phosphorus content, electrical conductivity, soil moisture, and ammonium nitrogen contents were the main factors. At the phylum level, the rhizosphere bacterial community composition was consistent, mainly included Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi. At the family level, the pecan plantations formed different rhizosphere enriched biomarkers due to the influence of soil type, with functional characteristics such as plant growth promotion and soil nutrient cycling. In addition, there existed low abundance core species such as Haliangiaceae, Bryobacteraceae, and Steroidobacteraceae. They played important roles in the rhizosphere environments through their functional characteristics and community linkages. Overall, this study provides a basis for the study of the rhizosphere microbiome in different soil types of pecan plantations, and plays an important role in the sustainable management of forest soil.

Resistance and Resilience of Fish Gut Microbiota to Silver Nanoparticles

Understanding mechanisms governing the resistance and resilience of microbial communities is essential for predicting their ecological responses to environmental disturbances. Although we have a good understanding of such issues for soil and lake ecosystems, how ecological resistance and resilience regulate the microbiota in the fish gut ecosystem remains unclear. Using the zebrafish model, we clarified the potential mechanisms governing the gut microbiota after exposure to silver nanoparticles (AgNPs). Here, we explored the ecological resistance and resilience of gut microbiota in zebrafish exposed to different concentrations of AgNPs (i.e., 10, 33 and 100 μg/liter) for 15, 45, 75 days. The high-throughput sequencing analysis of the 16S rRNA gene showed that AgNP exposure significantly reduced the α-diversity of gut microbiota and resulted in obvious dynamics of community composition and structure. However, the rebound of zebrafish gut microbiota was pushed toward an alternative state after 15 days of AgNP exposure. We found that homogeneous selection was a more prevalent contributor in driving gut community recovery after AgNP exposure. The resilience and resistance of gut microbiota responses to AgNP disturbance might be mainly determined by the predominant keystone taxa such as Acinetobacter and Gemmata. This study not only expanded our understanding of fish gut microbiota's responses to pollutants but also provided new insights into maintaining host-microbiome stability during environmental perturbations. IMPORTANCE Understanding the ecological mechanisms governing the resistance and resilience of microbial communities is a key issue to predict their responses to environmental disturbances. Using the zebrafish model, we wanted to clarify the potential mechanisms governing the resistance and resilience of gut microbiota after exposure to silver nanoparticles (AgNPs). We found that AgNP contamination significantly reduced the α-diversity of gut microbiota and resulted in obvious changes in community composition. The resilience and resistance of gut microbiota to AgNPs might be associated with the predominant keystone taxa (e.g., Acinetobacter and Gemmata). This study greatly expanded our understanding of how fish gut microbiota responds to environmental perturbations and maintains stability.