Temporal dynamics of microbial communities in microcosms in response to pollutants

Dissipation of pesticides and responses of bacterial, fungal and protistan communities in a multi-contaminated vineyard soil

The effect of pesticide residues on non-target microorganisms in multi-contaminated soils remains poorly understood. In this study, we examined the dissipation of commonly used pesticides in a multi-contaminated vineyard soil and its effect on bacterial, fungal, and protistan communities. We conducted laboratory soil microcosm experiments under varying temperature (20°C and 30°C) and water content (20 % and 40 %) conditions. Pesticide dissipation half-lives ranged from 27 to over 300 days, depending on the physicochemical properties of the pesticides and the soil conditions. In both autoclaved and non-autoclaved soil experiments, over 50 % of hydrophobic pesticides (dimethomorph > isoxaben > simazine = atrazine = carbendazim) dissipated within 200 days at 20°C and 30°C. However, the contribution of biodegradation to the overall dissipation of soluble pesticides (rac-metalaxyl > isoproturon = pyrimethanil > S-metolachlor) increased to over 75 % at 30°C and 40 % water content. This suggests that soluble pesticides became more bioavailable, with degradation activity increasing with higher temperature and soil water content. In contrast, the primary process contributing to the dissipation of hydrophobic pesticides was sequestration to soil. High-throughput amplicon sequencing analysis indicated that water content, temperature, and pesticides had domain-specific effects on the diversity and taxonomic composition of bacterial, fungal, and protistan communities. Soil physicochemical properties had a more significant effect than pesticides on the various microbial domains in the vineyard soil. However, pesticide exposure emerged as a secondary factor explaining the variations in microbial communities, with a more substantial effect on protists compared to bacterial and fungal communities. Overall, our results highlight the variability in the dissipation kinetics and processes of pesticides in a multi-contaminated vineyard soil, as well as their effects on bacterial, fungal, and protistan communities.

Fungal, but not bacterial, diversity and network complexity promote network stability during roadside slope restoration

To restore degraded roadside ecosystems, conventional methods such as revegetation and soil amendment are frequently employed. However, our understanding of the long-term effects of these restoration approaches on soil microbial diversity and network complexity across different vegetation types remains poor, which contributes to poor restoration outcomes. In this study, we explored the effects of roadside slope restoration on microbial communities across different vegetation types at varying stages of restoration. We found that restoration time had a more pronounced impact on microbial diversity than specific vegetation type. As restoration progressed, microbial network complexity and fungal diversity increased, but bacterial diversity declined, suggesting that keystone taxa may contribute to network complexity. Interestingly, bacterial network complexity increased concomitant with decreasing network modularity and robustness, which may compromise system stability. Distinct vegetation types were associated with restoration-sensitive microbial communities at different restoration stages. Leguminouse and nitrogen-fixing plants, such as Albiziak alkora, Ginkgo biloba, Rhus chinensis, Rhapis excels, and Rubia cordifolia exhibited such associations after five years of restoration. These keystone taxa included Proteobacteria, Actinobacteria, Chloroflexi, Gemmatimonadota, and Myxococcota. We also found that bacterial alpha diversity was significantly correlated with restoration time, soil pH, moisture, available phosphate, nitrate nitrogen, and plant height, while fungal diversity was primarily shaped by restoration time. Together, our findings suggest that soil properties, environmental factors, vegetation type, and dominant species can be manipulated to guide the trajectory of ecological recovery by regulating the abundance of certain microbial taxa.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

Metagenomics reveals the self-recovery and risk of antibiotic resistomes during carcass decomposition of wild mammals

Animal carcass decomposition may bring serious harm to the environment, including pathogenic viruses, toxic gases and metabolites, and antibiotic resistance genes (ARGs). However, how wild mammal corpses decomposition influence and change ARGs in the environment has less explored. Through metagenomics, 16S rRNA gene sequencing, and physicochemical analysis, this study explored the succession patterns, influencing factors, and assembly process of ARGs and mobile genetic elements (MGEs) in gravesoil during long-term corpse decomposition of wild mammals. Our results indicate that the ARG and MGE communities related to wildlife corpses exhibited a pattern of differentiation first and then convergence. Different from the farmed animals, the decomposition of wild animals first reduced the diversity of ARGs and MGEs, and then recovered to a level similar to that of the control group (untreated soil). ARGs and MGEs of the gravesoil are mainly affected by deterministic processes in different stages. MGEs and bacterial community are the two most important factors affecting ARGs in gravesoil. It is worth noting that the decomposition of wild animal carcasses enriched different high-risk ARGs at different stages (bacA, mecA and floR), which have co-occurrence patterns with opportunistic pathogens (Comamonas and Acinetobacter), thereby posing a great threat to public health. These results are of great significance for wildlife corpse management and environmental and ecological safety.

Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea

BACKGROUND

Declines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.

RESULTS

Our findings indicated a noteworthy decline in soil bacterial α-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal α-diversity. Additionally, we observed that the impact of shrub species richness on microbial α-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.

CONCLUSIONS

Our findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils. Video Abstract.

Sulfate reduction behavior in response to changing of pressure coupling with temperature inside landfill

The behavior of sulfate reduction, which was the source of hydrogen sulfide (H2S) odor, was investigated under changing pressure and temperature conditions inside landfills. The results showed that the release of H2S and methyl mercaptan (MM) was significantly inhibited at 25 °C and 50 °C under pressure, and the highest H2S and MM concentrations released were only 0.82 %-1.30 % and 1.87 %-4.32 % of atmospheric pressure, respectively. Analysis of the microbial community structure and identification of sulfate-reducing bacteria (SRB) revealed that temperature significantly altered the microbial community in the landfill environment, while pressure inhibited some bacteria and induced the growth and reproduction of specific bacteria. Key SRB (Desulfosporosinus-ASV212, Desulfitibacter-ASV1744) mediated differentiated sulfate reduction behavior in the pressure-bearing environment at 25 °C, while key SRB (Dethiobacter-ASV177, Desulfitibacter-ASV2355 and ASV316) were involved at 50 °C. This study provides a theoretical basis for the formulation of landfill gas management and control strategies.

Flooding drives the temporal turnover of antibiotic resistance gene in manure-amended soil-water continuum

Rice paddy soil is a hotspot of antibiotic resistance genes (ARGs) due to the application of organic fertilizers. However, the temporal dynamics of ARGs in rice paddy soil and its flooded water during the growing season remain underexplored. In this study, a microcosm experiment was conducted to explore the ARG profiles in a long term (130 days) flooded two-phase manure-amended soil-water system. By using high-throughput quantitative PCR array, a total of 23-98 and 34-85 ARGs were detected in the soil and overlying water, respectively. Regression analysis exhibited significant negative correlations between ARG profile similarities and flooding duration, indicating that flooding significantly altered the resistome (P < 0.001). This finding was validated by the increased ARG abundance in the soil and the overlying water, for example, after 130 days flooding, the abundance of ARGs in CK soil was increased from 0.03 to 1.20 copies per 16S rRNA. The PCoA analysis further suggested pig manure application resulted in distinct ARG profiles in the soil-water continuum compared with those of the non-amended control (Adonis, P < 0.05). The Venn diagram showed that all ARGs detected in the pig manure were present in the treated soil. Twelve ARGs (e.g., sul1) were shared among the pig manure, manure-amended soil, and overlying water, indicating that certain manure- or soil-borne ARGs were readily dispersed from the soil to the overlying water. Moreover, the enhanced relationships between the ARGs and mobile genetic elements in pig manure applied soil-water continuum indicate that the application of organic matter could accelerate the emergence and dissemination of ARGs. These findings suggested that flooding represents a crucial pathway for dispersal of ARGs from the soil to the overlying water. Identification of highly mobile ARGs in the soil-water continuum is essential for assessing their potential risk to human health and promoting the development of sustainable agricultural practices to mitigate their spread.

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.

Deep relationships between bacterial community and polycyclic aromatic hydrocarbons in soil profiles near typical coking plants

Bacterial communities play an important role in maintaining the normal functioning of ecosystems; therefore, it is important to understand the effects of polycyclic aromatic hydrocarbons (PAHs) on the bacterial community. In addition, understanding the metabolic potential of bacterial communities for PAHs is important for the remediation of PAH-contaminated soils. However, the deep relationship between PAHs and bacterial community in coking plants is not clear. In this study, we determined the bacterial community and the concentration of PAHs in three soil profiles contaminated by coke plants in Xiaoyi Coking Park, Shanxi, China, using 16S rRNA and gas chromatography coupled with mass spectrometry, respectively. The results show that 2 ~ 3 rings PAHs are the main PAHs and Acidobacteria (23.76%) was the dominant bacterial community in three soil profiles. Statistical analysis showed that there were significant differences in the composition of bacterial communities at different depths and different sites. Redundancy analysis (RDA) and variance partitioning analysis (VPA) illustrate the influence of environmental factors (including PAHs, soil organic matter (SOM), and pH) on the vertical distribution of soil bacterial community, and PAHs were the main factors affecting the bacterial community in this study. The co-occurrence networks further indicated correlations between bacterial community and PAHs and found that Nap has the greatest effect on bacterial community compared with other PAHs. In addition, some operational taxonomic units (OTUs, OTU2, and OTU37) have the potential to degrade PAHs. PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used for further study on the potential of microbial PAHs degradation from a genetic perspective, which showed that different PAH metabolism genes were present in the genomes of bacterial communities in the three soil profiles, and a total of 12 PAH degradation-related genes were isolated, mainly dioxygenase and dehydrogenase genes.

Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions

The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics. Higher additions of Bt toxins led to higher concentrations of soil organic matter (SOM), ammonium (NH⁺₄-N), and nitrite (NO₂^--N) compared against controls without addition after 100 days of soil incubation. High-throughput qPCR analysis and shotgun metagenomic sequencing analysis revealed that the 500 ng/g Bt toxin addition significantly affected profiles of soil microbial functional genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycling after 100 days of incubation. Furthermore, combined metagenomic and metabolomic analyses indicated that the 500 ng/g Bt toxin addition significantly altered low molecular weight metabolite profiles of soils. Importantly, some of these altered metabolites are involved in soil nutrient cycling, and robust associations were identified among differentially abundant metabolites and microorganisms due to Bt toxin addition treatments. Taken together, these results suggest that higher levels of Bt toxin addition can alter soil nutrients, probably by affecting the activities of Bt toxin-degrading microorganisms. These dynamics would then activate other microorganisms involved in nutrient cycling, finally leading to broad changes in metabolite profiles. Notably, the addition of Bt toxins did not cause the accumulation of potential microbial pathogens in soils, nor did it adversely affect the diversity and stability of microbial communities. This study provides new insights into the putative mechanistic associations among Bt toxins, soil characteristics, and microorganisms, providing new understanding into the ecological impacts of Bt toxins on soil ecosystems.

Metagenomics reveals the response of antibiotic resistance genes to elevated temperature in the Yellow River

Climate warming may aggravate the threat of antibiotic resistance genes (ARGs) to environmental and human health. However, whether temperature can predict ARGs and influence their assembly processes remains unknown. Here, we used metagenomic sequencing to explore how gradually elevated water temperature (23 °C, 26 °C, 29 °C, 32 °C, 35 °C) influences ARG and mobile genetic element (MGE) profiles in the Yellow River. In total, 30 ARG types including 679 subtypes were detected in our water samples. Gradually increased temperature remarkably reduced ARG diversity but increased ARG abundance. Approximately 37 % of ARGs and 42 % of MGEs were predicted by temperature, while most others were not sensitive to temperature. For each 1 °C increase in temperature, the ARG abundance rose by 2133 TPM (Transcripts Per kilobase of exon model per Million mapped reads) abundance, and multidrug, tetracycline and peptide resistance genes had the fastest increases. Proteobacteria and Actinobacteria were the primary ARG hosts, with 558 and 226 ARG subtypes, respectively. Although ARG profiles were mainly governed by stochastic process, elevated temperature increased the deterministic process of ARGs in the Yellow River. The abundance of five high-risk ARGs (tetM, mecA, bacA, vatE and tetW) significantly increased with elevated water temperature, and these ARGs co-occurred with several opportunistic pathogens (Delftia, Legionella and Pseudomonas), implying that antibiotic resistance risk may increase under climate warming. Our study explored the possibility of predicting resistomes and their health risks through temperature, providing a novel approach to predict and control ARGs in water environments under climate warming.

Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water

Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.

Soil mesofauna alter the balance between stochastic and deterministic processes in the plastisphere during microbial succession

Plastic debris, as a novel substrate, provides an avenue for enriching microbial growth. Although the structure of the aquatic plastisphere microbial community is well-characterised, linkages between microbial community assembly and species co-existence in the soil plastisphere vary and remain poorly understood, particularly when soil fauna is involved. This study investigated the soil plastisphere community, including bacteria, fungi, and protists, focusing on microbial succession and community assembly processes impacted by soil mesofauna. Certain soil plastisphere microbial taxa thrived at particular time points (e.g. Actinobacteria at 60 d), indicating the irreplaceable role of microplastic selection for time-sensitive taxa. Additionally, the biodiversity of keystone ecological clusters in the soil plastisphere was significantly associated with incubation time. Furthermore, the slopes of bacterial and fungal time-decay curves in soil plastisphere were steeper when treated with soil mesofauna than without soil mesofauna, whereas protist time-decay curves (total and abundant taxa) exhibited the opposite trend. Soil mesofauna increased the relative importance of determinacy in the soil plastisphere bacterial assembly process, while enhancing the stochasticity of fungal and protistan community assemblages. The study demonstrates the complex assembly patterns of soil plastisphere microbial communities, emphasising the importance of interactions between the plastisphere and local soil fauna from an ecological perspective.

Effects of different colored polyethylene mulching films on bacterial communities from soil during enrichment incubation

Studies have shown that mulching agricultural fields with plastic residues can influence microbial communities in the environment, but few studies have investigated the differences in the soil microbial communities in distinct areas under mulching with different colored plastic products. Thus, in this study, we explored how different colored polyethylene mulching films (PMFs) might affect soil bacterial communities during enrichment incubation. We found significant differences in the bacterial communities under different colored PMFs after incubation. Treatment with the same colored PMF obtained more similar bacterial community compositions. For instance, at the class level, Gammaproteobacteria and Bacteroidia were most abundant with black PMF, whereas Actinobacteria and Bacteroidia were most abundant with white PMF. The most abundant genera were Acinetobacter and Chryseobacterium with black PMF but Rhodanobacter and Paenarthrobacter with white PMF. Polyethylene- and hydrocarbon-degrading bacteria were the core members detected under both treatments, and the bacterial communities were predicted to have the potential for the biodegradation and metabolism of xenobiotics after enrichment culture according to the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) tool. In addition, the bacterial communities in soil from Xinjiang treated with white PMF and in soil from Yangling treated with black PMF were strongly correlated and stable. Our results suggest that the color of the PMF applied affected the soil bacterial communities, where plastics with the same color may have recruited similar species of microorganisms, although the origins of these microorganisms were not the same.

Resilience of the wheat root-associated microbiome to the disturbance of phenanthrene

The microbial communities are of high importance to the restoration of ecological function and plant health, while little information about the influence of exogenous pollutants on the resilience and temporal dynamics of root microbial communities is available. In this study, a greenhouse experiment was conducted to investigate the effects of exogenous phenanthrene in terms of time and pollution disturbance on the wheat root-associated microbial communities. It was found that a high phenanthrene degradation rate of 86 % was achieved in the rhizosphere of wheat after the first-week planting. Compared to phenanthrene pollution, temporal changes had more significant impacts on the wheat root microbial communities. Obvious change of microbes influenced by PHE had been revealed at the initial three-week planting even most of PHE has been degraded, and the enriched microbes in the rhizosphere were affiliated to Altererythrobacter, Massilia, Mycobacterium, Ramlibacter, Sphingobium, Novosphingobium and Romboutsia. However, at the later stage after four-week incubation, the wheat root-associated microbial communities gradually recovered to the state without pollution. The results of this study were helpful to deepen the understanding of the response of root-associated microbial resilience to the exogenous phenanthrene pollution, and would benefit the stability and balance of agricultural ecology facing exogenous organic pollutants.

Ruminal Bacterial Community Successions in Response to Monensin Supplementation in Goats

Simple Summary

Monensin has been successfully used in the ruminants’ diets to manipulate ruminal fermentation and improve feed efficiency, but its use is facing decreased levels of social acceptance due to the potential impacts on public health. Understanding the ruminal bacterial community successions in response to monensin supplementation would help the search for alternatives. We found that the ruminal ecosystem was reshaped through a series of succession processes during the adaption to monensin rather than following a clear dichotomy between Gram-positive and Gram-negative cell types, and the carbohydrate-degrading bacteria presented a higher adaptability. Therefore, a potential alternative for monensin as a rumen modifier could be one with similar patterns of ruminal microbial community successions.

Abstract

Previous studies have demonstrated that the effects of monensin on methanogenesis and ruminal fermentation in ruminants were time-dependent. To elucidate the underlying mechanism, we investigated the ruminal bacterial community successions during the adaptation to monensin supplementation and subsequent withdrawal in goats. The experiment included a baseline period of 20 days followed by a treatment period of 55 days with 32 mg monensin/d and a washout period of 15 days. Monensin supplementation reduced the α diversity and changed the structure of ruminal microflora. The α diversity was gradually restored during adaption, but the structure was still reshaped. The temporal dynamics of 261 treatment- and/or time-associated ruminal bacteria displayed six patterns, with two as monensin-sensitive and four as monensin-resistant. The monensin sensitivity and resistance of microbes do not follow a clear dichotomy between Gram-positive and Gram-negative cell types. Moreover, the temporal dynamic patterns of different bacterial species within the same genus or family also displayed variation. Of note, the relative abundance of the total ruminal cellulolytic bacteria gradually increased following monensin treatment, and that of the total amylolytic bacteria were increased by monensin, independent of the duration. In conclusion, under the pressure of monensin, the ruminal ecosystem was reshaped through a series of succession processes, and the carbohydrate-degrading bacteria presented a higher level of adaptability.

Stronger responses of soil protistan communities to legacy mercury pollution than bacterial and fungal communities in agricultural systems

Soil pollution is an important stressor affecting biodiversity and ecosystem functioning. However, we lack a holistic understanding of how soil microbial communities respond to heavy metal pollution in agricultural ecosystems. Here, we explored the distribution patterns and inter-kingdom interactions of entire soil microbiome (including bacteria, fungi, and protists) in 47 paired paddy and upland fields along a gradient of legacy mercury (Hg) pollution. We found that the richness and composition of protistan community had stronger responses to Hg pollution than those of bacterial and fungal communities in both paddy and upland soils. Mercury polluted soils harbored less protistan phototrophs but more protistan consumers. We further revealed that long-term Hg pollution greatly increased network complexity of protistan community than that of bacterial and fungal communities, as well as intensified the interactions between protists and the other microorganisms. Moreover, our results consistently indicated that protistan communities had stronger responses to long-term Hg pollution than bacterial and fungal communities in agricultural soils based on structural equation models and random forest analyses. Our study highlights that soil protists can be used as bioindicators of Hg pollution, with important implications for the assessment of contaminated farmlands and the sustainable management of agricultural ecosystems.

Effect of microplastics on microbial dechlorination of a polychlorinated biphenyl mixture (Aroclor 1260)

Microplastics (MPs) and polychlorinated biphenyls (PCBs) generally coexist in the environment, posing risks to public health and the environment. This study investigated the effect of different MPs on the microbial anaerobic reductive dechlorination of Aroclor 1260, a commercial PCB mixture. MP exposure inhibited microbial reductive dechlorination of PCBs, with inhibition rates of 39.43%, 23.97%, and 17.53% by polyethylene (PE), polypropylene (PP), and polystyrene (PS), respectively. The dechlorination rate decreased from 1.63 μM Cl^- d^-1 to 0.99-1.34 μM Cl^- d^-1 after MP amendment. Chlorine removal in the meta-position of PCBs was primarily inhibited by MPs, with no changes in the final PCB dechlorination metabolites. The microbial community compositions in MP biofilms were not significantly different (P > 0.05) from those in suspension culture, although possessing greater Dehalococcoides abundance (0.52-0.81% in MP biofilms; 0.03-0.12% in suspension culture). The co-occurrence network analysis revealed that the presence of MPs attenuated microbial synergistic interactions in the dechlorinating culture systems, which may contribute to the inhibitory effect on microbial PCB dechlorination. These findings are important for comprehensively understanding microbial dechlorination behavior and the environmental fate of PCBs in environments with co-existing PCBs and MPs and for guiding the application of in situ PCB bioremediation.

What will polyethylene film mulching bring to the root-associated microbial community of Paeonia ostii?

Plastic film mulching can increase crop yield and is widely used in agricultural production, but long-term mulching could adversely affect plant growth. To investigate the related mechanism, we studied the bacterial communities in different root-associated compartments of Paeonia ostii, a perennial oil crop, under polyethylene film mulching for three years by full-length 16S rDNA sequencing technology, and measured the soil physicochemical properties and enzyme activities. We found that enzyme activities and available nutrients in the soil tended to decrease after long-term mulching. Analysis of bacterial community composition revealed that the endosphere may be another potential source of the root-associated microbiome of P. ostii, and the rhizoplane plays a selective gating role in the enrichment processes for P. ostii microbiome assembly. Long-term mulching affected the abundance of dominant bacterial communities in different root-associated compartments and reduced the bacterial richness in the endosphere, but increased bacterial interactions in each compartment, as well as between different compartments. We speculate that this is mainly related to the decrease of litter content and the serious degradation of polyethylene film after long-term mulching, which resulted in microplastics and other harmful substances entering the soil. Our study further explained the reasons for the harm of long-term film mulching on plants to guide the rational use of plastic film. KEY POINTS: •Soil enzyme activities and available nutrients decreased after long-term mulching. •Mulching affected the dominant bacterial abundance in different root-associated compartments. •Mulching increased bacterial interactions among compartments.

Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation

Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.

Sulfate-reduction behavior in waste-leachate transition zones of landfill sites

The sulfate reduction behavior of the waste-leachate transition zone of landfill was investigated at different temperatures and moisture contents. Marked differences in the sulfate reduction behavior were observed in the waste-leachate transition zone. The highest H₂S concentration was observed when the solid-to-liquid ratio was 1:3 at both temperatures. Although more leachate led to higher H₂S concentrations, the solid-to-liquid ratio was likely of subordinate significance compared with temperature. The microbial community was more unstable at 50 °C and more extensive mutualistic interactions among bacteria were observed, resulting in SRB showing a more violent response to changes in the solid-to-liquid ratio. At 25 °C, it's the opposite. A temperature of 25 °C was suitable for most SRB (such as Desulfomicrobium and Desulfobulbus), while some specific SRB that did not contain the functional genes (such as Dethiobacter and Anaerolinea) played a pivotal role in the significant differences in sulfate reduction behavior observed at 50 °C. This study provides a theoretical basis for controlling the release of H₂S from landfill.

The effect of combined pollution by PAHs and heavy metals on the topsoil microbial communities of Spolic Technosols of the lake Atamanskoe, Southern Russia

The contamination with organic and inorganic pollutants changes significantly soil microbial community structure. These shifts indicate anthropogenic pressure and help to discover new possibilities for soil remediation. In this study, the microbial community structure of Spolic Technosols formed at the territory of a former industrial sludge reservoir near the Kamensk-Shakhtinsky (Southern Russia) was studied using a metagenomics approach. The studied soils contain high concentrations of heavy metals (HM) (up to 72,900 mg kg^-1) and 16 priority polycyclic aromatic hydrocarbons (PAHs) (up to 6670 mg kg^-1). Its microbial communities demonstrate an excellent adaptability level reflected in their complexity and diversity. As shown by the high values of alpha diversity indices (Shannon values up to 10.1, Chao1 values from 1430 to 4273), instead of decreasing quantitatively and qualitatively on the systemic level, microbial communities tend to undergo complex redistribution. Regardless of contamination level, the share of Actinobacteria and Proteobacteria was consistently high and varied from 20 to 50%. Following the results of the Mann-Whitney U test, there were significant changes of less abundant phyla. The abundance of oligotrophic bacteria from Gemmatimonadetes and Verrucomicrobia phyla and autotrophic bacteria (e.g., Nitrospira) decreased due to the high PAH's level. And abundance of Firmicutes and amoebae-associated bacteria such as TM6 and soil Chlamydia increased in highly contaminated plots. In the Spolic Technosols studied, the influence of factors on the microbial community composition decreased from PAHs concentration to soil characteristics (organic carbon content) and phylum-phylum interactions. The high concentrations of HMs influenced weakly on the microbial community composition.

Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections

Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while r-ones would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments' land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating from fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.

Bacterial Community Structure and Metabolic Function Succession During the Composting of Distilled Grain Waste

Distilled grain waste (DGW) can be converted to organic fertilizer via aerobic composting process without inoculating exogenous microorganisms. To illustrate the material conversion mechanism, this study investigated the dynamic changes of bacterial community structure and metabolic function involved in DGW composting. Results showed that a significant increase in microbial community alpha diversity was observed during DGW composting. Moreover, unique community structures occurred at each composting stage. The dominant phyla were Firmicutes, Proteobacteria, Actinobacteriota, Bacteroidota, Myxococcota, and Chloroflexi, whose abundance varied according to different composting stages. Keystone microbes can be selected as biomarkers for each stage, and Microbispora, Chryseolinea, Steroidobacter, Truepera, and Luteimonas indicating compost maturity. Co-occurrence network analysis revealed a significant relationship between keystone microbes and environmental factors. The carbohydrate and amino acid metabolism were confirmed as the primary metabolic pathways by metabolic function profiles. Furthermore, nitrogen metabolism pathway analysis indicated that denitrification and NH₃ volatilization induced higher nitrogen loss during DGW composting. This study can provide new understanding of the microbiota for organic matter and nitrogen conversion in the composting process of DGW.

Substrate type and plant phenolics influence epiphytic bacterial assembly during short-term succession

In natural ecosystems, large amounts of epiphytic bacteria live on the surfaces of submerged plants or non-biological substrates. Although it contributes greatly to host plant health or ecological functions in waters, little is known about the temporal dynamics and assembly mechanisms of epiphytic bacteria. To test whether host plant chemistry leads to divergent community dynamics, we investigated the fine scale temporal community successions of both epiphytic bacteria and the bacterioplankton of the surrounding water in two submerged plants and one non-biological artificial substance. We first observed differentiated epiphytic or surrounding water bacterial communities for different substrates in small spaces (approximately 1 m × 1 m). Selection played dominant roles in affecting the assembly of epiphytic bacteria in the high-phenolic plant Hydrilla verticillata, while for the artificial substance and the low-phenolic plant Vallisneria natans, drift and dispersal drove the assembly of both epiphytic bacteria and bacterioplankton. The higher selection may also contribute to higher turnover rates in both bacterioplankton and epiphytic communities of H. verticillata, with the latter changing drastically in approximately one week. Epiphytic bacteria in H. verticillata developed more complex networks with a higher proportion of positive links, suggesting that more intense interactions such as mutualism or facilitation may exist within epiphytic bacterial communities of the high-phenolic plant. Our results also implied that for the submerged macrophytes used in biological purification, the dynamics of epiphytic biofilm in the purification-related functional capacities might also be considered.

Changes in Soil Microbial Communities across an Urbanization Gradient: A Local-Scale Temporal Study in the Arid Southwestern USA

Urban development is one of the leading causes of biodiversity change. Understanding how soil microorganisms respond to urbanization is particularly important because they are crucial for the provisioning of ecosystem functions and services. Here, we collected monthly soil samples over one year across three locations representing an urbanization gradient (low-moderate-high) in the arid Southwestern USA, and we characterized their microbial communities using marker gene sequencing. Our results showed that microbial richness and community composition exhibited nonsignificant changes over time regardless of the location. Soil fungal richness was lower in moderately and highly urbanized locations, but soil bacterial/archaeal richness was not significantly different among locations. Both bacteria/archaea and fungi exhibited significant differences in community composition across locations. After inferring potential functional groups, soils in the highly urbanized location had lower proportions of arbuscular mycorrhizal fungi and soil saprotrophic fungi but had higher proportions of bacterial taxa involved in aromatic compound degradation, human pathogens, and intracellular parasites. Furthermore, ammonia-oxidizing bacteria were more abundant in the highly urbanized location, but ammonia-oxidizing archaea were more abundant in lowly and moderately urbanized locations. Together, these results highlight the significant changes in belowground microbial communities across an urbanization gradient, and these changes might have important implications for aboveground–belowground interactions, nutrient cycling, and human health.

Seasonal and spatial variation of protist communities from reef water and open ocean water in patchy coral reef areas of a semi-enclosed bay

Protists are an important component of the marine ecosystem and play an essential role in material cycle and energy flow, but the distribution of protists in coral reefs have not been fully studied. In this study, high-throughput amplicon sequencing technology was used to study the biodiversity and community structure of protists from coral reefs and open sea areas, with the typical semi-enclosed bay Daya Bay as the research field. There were significant seasonal differences in the dominant phyla of protists, biodiversity index values and βeta diversity (P < 0.05) but no significant differences in the different sampling areas (P > 0.05). The topological parameters of the co-occurrence network showed the protist co-occurrence network in the open sea had more complex interactions and stronger stability than in the coral reef areas because of the hydrodynamics, waves, and relatively poor nutrients. Redundancy analysis and the Mantel test showed that the structure of the protist community was affected by seawater temperature, pH, salinity, and dissolved oxygen. This study analysed the temporal and spatial differences in protists in the coral reef and open sea areas of Daya Bay to provide important information for the study of protist biodiversity and community structure in semi-enclosed bays.

Characterization and Performance of Lactate-Feeding Consortia for Reductive Dechlorination of Trichloroethene

Understanding the underlying mechanism that drives the microbial community mediated by substrates is crucial to enhance the biostimulation in trichloroethene (TCE)-contaminated sites. Here, we investigated the performance of stable TCE-dechlorinating consortia by monitoring the variations in TCE-related metabolites and explored their underlying assembly mechanisms using 16S rDNA amplicon sequencing and bioinformatics analyses. The monitoring results indicated that three stable TCE-dechlorinating consortia were successfully enriched by lactate-containing anaerobic media. The statistical analysis results demonstrated that the microbial communities of the enrichment cultures changed along with time and were distinguished by their sample sources. The deterministic and stochastic processes were simultaneously responsible for shaping the TCE-dechlorinating community assembly. The indicator patterns shifted with the exhaustion of the carbon source and the pollutants, and the tceA-carrying Dehalococcoides, as an indicator for the final stage samples, responded positively to TCE removal during the incubation period. Pseudomonas, Desulforhabdus, Desulfovibrio and Methanofollis were identified as keystone populations in the TCE-dechlorinating process by co-occurrence network analysis. The results of this study indicate that lactate can be an effective substrate for stimulated bioremediation of TCE-contaminated sites, and the reduction of the stochastic forces or enhancement of the deterministic interventions may promote more effective biostimulation.

Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium

BACKGROUND

Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species.

RESULTS

In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria.

CONCLUSIONS

We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.

Polycyclic aromatic hydrocarbon and n-alkane pollution characteristics and structural and functional perturbations to the microbial community: a case-study of historically petroleum-contaminated soil

Characterization of the typical petroleum pollutants, polycyclic aromatic hydrocarbons (PAHs) and n-alkanes, and indigenous microbial community structure and function in historically contaminated soil at petrol stations is critical. Five soil samples were collected from a petrol station in Beijing, China. The concentrations of 16 PAHs and 31 n-alkanes were measured by gas chromatography-mass spectrometry. The total concentrations of PAHs and n-alkanes ranged from 973 ± 55 to 2667 ± 183 μg/kg and 6.40 ± 0.38 to 8.65 ± 0.59 mg/kg (dry weight), respectively, which increased with depth. According to the observed molecular indices, PAHs and n-alkanes originated mostly from petroleum-related sources. The levels of ΣPAHs and the total toxic benzo[a]pyrene equivalent (ranging from 6.41 to 72.54 μg/kg) might exert adverse biological effects. Shotgun metagenomic sequencing was employed to investigate the indigenous microbial community structure and function. The results revealed that Proteobacteria and Actinobacteria were the most abundant phyla, and Nocardioides and Microbacterium were the important genera. Based on COG and KEGG annotations, the highly abundant functional classes were identified, and these functions were involved in allowing microorganisms to adapt to the pressure from contaminants. Five petroleum hydrocarbon degradation-related genes were annotated, revealing the distribution of degrading microorganisms. This work facilitates the understanding of the composition, source, and potential ecological impacts of residual PAHs and n-alkanes in historically contaminated soil.

Response of microbial community to the lysis of Phaeocystis globosa induced by a biological algicide, prodigiosin

Terminating harmful algal blooms by using algicidal agents is a strong disturbance event in marine environment, which has powerful structural influences on microbial ecosystems. But, the response of microbial ecosystem to algicidal agent is largely unknown. Here, we conducted Phaeocystis globosa microcosms to investigate the dynamics, assembly processes, and co-occurrence patterns of microbial communities in response to algicidal process induced by a highly efficient algicidal agent, prodigiosin, by using 16S rRNA gene amplicon sequencing. The α-diversity of microbial community showed no obvious changes during the algicidal process in P. globosa microcosm treated with prodigiosin (group PD). Rhodobacteraceae increased significantly (P < 0.05) during algicidal process in PD, and this was mainly due to the lysis of P. globosa cells. Compared to the control group, the temporal turnover rates of common and rare taxa in PD were significantly higher because of the lysis of P. globosa induced by prodigiosin. Neutral processes mainly drove the assembly of microbial communities in all microcosms, even though the algicidal process induced by prodigiosin had no effect on the assembly processes. In addition, the time-decay relationship and co-occurrence network analysis indicate that rare taxa play important roles in maintaining microbial community stability in response to the algicidal process, rather than prodigiosin. These findings suggest that prodigiosin cannot affect the dynamics of microbial communities directly; however, future investigations into the function of microbial communities in response to prodigiosin remain imperative.

Effects of N-acyl-homoserine lactones-based quorum sensing on biofilm formation, sludge characteristics, and bacterial community during the start-up of bioaugmented reactors

Bioaugmentation is an effective technology for treating wastewater containing recalcitrant organic pollutants. However, it is restricted by several technical problems, including the difficult colonization and survival of the inoculated bacteria, and the time-consuming start-up process. Considering the important roles of quorum sensing (QS) in regulating microbial behaviors, this study investigated the effects of N-acyl-homoserine lactones (AHLs)-based manipulation on the start-up of biofilm reactors bioaugmented with a pyridine-degrading strain Paracoccus sp. BW001. The results showed that, in the presence of two specific exogenous AHLs (C6-HSL and 3OC6-HSL), the biofilm formation process on carriers was significantly accelerated, producing thick and structured biofilms. The protein and polysaccharide contents of the extracellular polymeric substances (EPS) and soluble microbial products (SMP) in sludge were also elevated, possibly due to the increased abundance of several EPS-producing bacterial genera. Specifically, the stability and complexity of protein structures were improved. Besides the reactor running time, the AHL-manipulation was proved to be the main factor that drove the shift of bacterial community structures in the reactors. The addition of exogenous AHLs significantly increased the succession rate of bacterial communities and decreased the bacterial alpha diversity. Most importantly, the final proportions of the inoculated strain BW001 were elevated by nearly 100% in both sludge and biofilm communities via the AHL-manipulation. These findings strongly elucidated that AHL-based QS was deeply involved in biofilm formation, sludge characteristics, and microbial community construction in bioaugmented reactors, providing a promising start-up strategy for bioaugmentation technology.

Soil potassium is correlated with root secondary metabolites and root-associated core bacteria in licorice of different ages

AIMS

Licorice (Glycyrrhiza uralensis Fisch.) is a crucial medicinal herb as it accumulates glycyrrhizin and liquiritin in roots. Licorice root-associated bacterial communities shaped by soil characteristics are supposed to regulate the accumulation of root secondary metabolites.

METHODS

The soil characteristics, root secondary metabolites, and root-associated bacterial communities were analyzed in licorice plants of different ages to explore their temporal dynamics and interaction mechanisms.

RESULTS

Temporal variation in soil characteristics and root secondary metabolites was distinct. The alpha-diversity of root-associated bacterial communities decreased with root proximity, and the community composition was clustered in the rhizosphere. Different taxa that were core-enriched from the dominant taxa in the bulk soil, rhizosphere soil, and root endosphere displayed varied time-decay relationships. Soil total potassium (TK) as a key factor regulated the temporal variation in some individual taxa in the bulk and rhizosphere soils; these taxa were associated with the adjustment of root secondary metabolites across different TK levels.

CONCLUSIONS

Licorice specifically selects root-associated core bacteria over the course of plant development, and TK is correlated with root secondary metabolites and individual core-enriched taxa in the bulk and rhizosphere soils, which may have implications for practical licorice cultivation.

LDPE microplastics significantly alter the temporal turnover of soil microbial communities

Although the ubiquitous presence of microplastics in various environments is increasingly well studied, knowledge of the effects of microplastics on ambient microbial communities is still insufficient. To estimate the response of soil bacterial community succession and temporal turnover to microplastic amendment, a soil microcosm experiment was carried out with polyethylene microplastics. The soil samples under control and microplastic amendment conditions were collected for sequencing analysis using Illumina MiSeq technology. Microplastic amendment was found to significantly alter soil bacterial community structure, and the community differences were increased linearly with the incubation time. Compared with the turnover rate of bacterial community in the control samples (0.0103, p < .05, based on Bray-Curtis similarity), the succession rate was significantly (p < .001) higher in the soil with microplastic amendment (0.0309, p < .001). In addition, the effects of microplastic amendment on the time-decay relationships (TDRs) on taxonomic divisions revealed considerable variations of TDRs values, indicating the effects were lineage dependent. Our results propose that the presence of microbial in soil ecosystem may lead to a faster succession rate of soil bacterial community, which provides new insights into the evolutionary consequences of microplastics in terrestrial environment.

Co-selection of antibiotic-resistant bacteria in a paddy soil exposed to As(III) contamination with an emphasis on potential pathogens

The increased acquisition of antibiotic resistance by pathogens is a global health concern. The environmental selection of antibiotic resistance can be caused by either antibiotic residues or co-selecting agents such as toxic metal(loid)s. This study explored the potential role of As(III) as a co-selecting driver in the spread of antibiotic resistance in paddy soils. By applying high-throughput sequencing, we found that the diversity and composition of soil microbial communities was significantly altered by As(III) exposure, resulting in an increased proportion of potential pathogens (9.9%) compared to the control soil (0.1%). Meanwhile, a total of 46 As(III)-resistant isolates were obtained from As(III)-exposure soil, among which potential pathogens accounted for 54.3%. These As(III)-resistant bacteria showed a high incidence of resistance to sulfanilamide (100%) and streptomycin (88-93%). The association between antibiotic and As(III) resistances was further investigated in a potentially pathogenic isolate by whole-genome sequencing and a transcription assay. The results showed that As(III) and antibiotic resistance genes might co-occur in a mobile genomic island and be co-regulated by As(III), implying that antibiotic resistance could be co-selected by As(III) via co-resistance and co-regulation mechanisms. Overall, these results suggest that As(III) exposure provides a strong selective pressure for the expansion of soil bacterial resistome.

Monitoring, assessment, and prediction of microbial shifts in coupled catalysis and biodegradation of 1,4-dioxane and co-contaminants

Microbial community dynamics were characterized following combined catalysis and biodegradation treatment trains for mixtures of 1,4-dioxane and chlorinated volatile organic compounds (CVOCs) in laboratory microcosms. Although a few specific bacterial taxa are capable of removing 1,4-dioxane and individual CVOCs, many microorganisms are inhibited when these contaminants are present in mixtures. Chemical catalysis by tungstated zirconia (WO_x/ZrO₂) and hydrogen peroxide (H₂O₂) as a non-selective treatment was designed to achieve nearly 20% 1,4-dioxane and over 60% trichloroethene and 50% dichloroethene removals. Post-catalysis, bioaugmentation with 1,4-dioxane metabolizing bacterial strain,Pseudonocardia dioxanivorans CB1190, removed the remaining 1,4-dioxane. The evolution of the microbial community under different conditions was time-dependent but relatively independent of the concentrations of contaminants. The compositions of microbiomes tended to be similar regardless of complex contaminant mixtures during the biodegradation phase, indicating a r-K strategy transition attributed to the shock experienced during catalysis and the subsequent incubation. The originally dominant genera Pseudomonas and Ralstonia were sensitive to catalytic oxidation, and were overwhelmed by Sphingomonas, Rhodococcus, and other catalyst-tolerant microbes, but microbes capable of biodegradation of organics thrived during the incubation. Methane metabolism, chloroalkane-, and chloroalkene degradation pathways appeared to be responsible for CVOC degradation, based on the identifications of haloacetate dehalogenases, 2-haloacid dehalogenases, and cytochrome P450 family. Network analysis highlighted the potential interspecies competition or commensalism, and dynamics of microbiomes during the biodegradation phase that were in line with shifting predominant genera, confirming the deterministic processes guiding the microbial assembly. Collectively, this study demonstrated that catalysis followed by bioaugmentation is an effective treatment for 1,4-dioxane in the presence of high CVOC concentrations, and it enhanced our understanding of microbial ecological impacts resulting from abiotic-biological treatment trains. These results will be valuable for predicting treatment synergies that lead to cost savings and improve remedial outcomes in short-term active remediation as well as long-term changes to the environmental microbial communities.

The distinct response of phenanthrene enriched bacterial consortia to different PAHs and their degradation potential: a mangrove sediment microcosm study

Understanding the microbial community succession to polycyclic aromatic hydrocarbons (PAHs) and identification of important degrading microbial groups are crucial for the designing of appropriate bioremediation strategies. In the present study, two distinct phenanthrene enriched bacterial consortia were treated against high molecular weight (Pyrene, Benzo (a) pyrene and Benzo (a) fluoranthene) and the response was studied in term of taxonomic variations by using High Throughput Illumina sequencing and qPCR analysis. Overall, the type of PAHs significantly affected the composition and the relative abundance of bacterial communities while no obvious difference was detected between bacterial communities of benzo (a) pyrene and benzo (a) fluoranthene treatments. Genera, Novosphingobium, Pseudomonas, Flavobacterium, Mycobacterium, Hoeflae, and Algoriphagus dominated all PAHs treatment groups indicating that they could be the key PAHs degrading phylotypes. Due to the higher abundance of gram-negative PAH-ring hydroxylating dioxygenase gene than that of gram-positive bacteria in all treated groups, we speculated that gram-negative bacteria may contribute more in the PAH degradation. The studied sediments harbored rich PAHs degrading bacterial assemblages involved in both low and high molecular weight PAHs and these findings provided new insight into the perspective of microbial PAHs bioremediation in the mangrove ecosystem.

Subsoil microbial community responses to air exposure and legume growth depend on soil properties across different depths

Anthropogenic disturbance, such as agricultural and architectural activities, can greatly influence belowground soil microbes, and thus soil formation and nutrient cycling. The objective of this study was to investigate microbial community variation in deep soils affected by strong disturbances. In present study, twelve soil samples were collected from different depths (0–300 cm) and placed onto the surface. We investigated the structure variation of the microbial community down through the soil profiles in response to disturbance originated by legume plants (robinia and clover) cultivation vs. plant-free controls. The high-throughput sequencing of 16S rRNA genes showed that microbial α-diversity decreased with depth, and that growing both plants significantly impacted the diversity in the topsoil. The soil profile was clustered into three layers: I (0–40 cm), II (40–120 cm), and III (120–300 cm); with significantly different taxa found among them. Soil properties explained a large amount of the variation (23.5%) in the microbial community, and distinct factors affected microbial assembly in the different layers, e.g., available potassium in layer I, pH and total nitrogen in layer II, pH and organic matter in layer III. The prediction of metabolic functions and oxygen requirements indicated that the number of aerobic bacteria increased with more air exposure, which may further accelerate the transformation of nitrogen, sulfur, carbon, and pesticides in the soil. The diversity of soil microorganisms followed a depth-decay pattern, but became higher following legume growth and air exposure, with notable abundance variation of several important bacterial species, mainly belonging to Nitrospira, Verrucomicrobia, and Planctomycetes, and soil properties occurring across the soil profiles.

Water-soluble phosphorus contributes significantly to shaping the community structure of rhizospheric bacteria in rocky desertification areas

Microorganisms play important roles in soil improvement. Therefore, clarifying the contribution of environmental factors in shaping the microbial community structure is beneficial to improve soil fertility in karst rocky desertification areas. Here, the bacterial community structures of eight rhizospheric soil samples collected from perennial fruit plantations were analysed using an Illumina HiSeq2500 platform. The diversity and abundance of bacteria in rocky desertification areas were significantly lower than those in non-rocky desertification areas, while the bacterial community structure was not significantly different between root surface and non-root surface soils in the same rhizospheric soil samples. Proteobacteria predominated in rocky desertification areas, while Actinobacteria predominated in non-rocky desertification areas. Correlation analysis revealed that water-soluble phosphorus content (r² = 0.8258), latitude (r² = 0.7556), altitude (r² = 0.7501), and the age of fruit trees (r² = 0.7321) were positively correlated with the bacterial community structure, while longitude, pH, and total phosphorus content did not significantly influence the soil bacterial community structure. As water-soluble phosphorus content is derived from insoluble phosphorus minerals, supplementing phosphorus-solubilising bacteria to soils in rocky desertification areas is a feasible strategy for accelerating the dissolution of insoluble phosphorus minerals and improving agricultural production and environment ecology.

Sedimentary DNA reveals over 150 years of ecosystem change by human activities in Lake Chao, China

Understanding the extent and directionality of the impact of human activities on ecosystems is directly related to their management and protection. However, the lack of historical data limits our understanding of ecosystem changes with long-term exposure to human activities. Recently, lake sedimentary DNA (sedDNA) has become a powerful tool for revealing changes in ecosystems at the century and millennium scales. Here, we used sedDNA to reveal the dynamic of the microbial community (including bacteria and micro-eukaryotes) in Lake Chao over the past 150 years, and further explored the effects of long-term nutrient and heavy metal loads on these communities. Our data show that nutrient and heavy metal loads in Lake Chao have increased by ca. 2 to 4-fold since the 1960s. In response, the community structure, diversity, and ecological network of bacteria and micro-eukaryotes changed significantly during the 1960s, the 1980s and the 2010s. Importantly, community structure was more sensitive to human activities than diversity. We also found that the relative abundance of some taxa associated with nitrification and algal blooms (e.g., taxa in Nitrospira sp., Peridinales) has increased ca. 100-fold since the 1960s. Nutrient could better explain the variation in the bacterial community (ca. twice as much as heavy metal), while heavy metal explained micro-eukaryotes better (ca. 3 or 5-fold as much as nutrient). In particular, based on parsimonious models from distance-based linear model (distLM), we further identified that Pb is the key factor affecting the bacterial and micro-eukaryotes community in Lake Chao in addition to nutrient. Our study reveals the impacts of long-term human activities on lake ecosystems from multiple perspectives of nutrient and heavy metal loads, community structure, diversity and ecological network, these findings will contribute to the management and conservation of lakes in the future.

Marine biofilm bacterial community response and carbon steel loss following Deepwater Horizon spill contaminant exposure

Steel marine structures provide foci of biodiversity when they develop into artificial reefs. Development begins with deposition of a biofilm. The effects of contaminants from oil spills on biofilm microbiomes, microbially-induced corrosion (MIC) and metal loss may impact preservation of marine metal structures. A microcosm experiment exposed biofilms on carbon steel disks (CSDs) to crude oil, dispersant, and dispersed oil to address their impacts on bacterial composition and metal loss and pitting. Biofilm diversity increased over time in all exposures. Community composition in dispersant and dispersed oil treatments deviated from the controls for the duration of a 12-week experiment. As biofilms matured, Pseudomonadaceae increased while Rhodobacteraceae decreased in abundance in dispersed oil treatments compared to the controls and dispersant treatments. Greatest mass loss and deepest pitting on CSDs were observed in dispersed oil treatments, suggesting impacts manifest as a consequence of increased MIC potential on carbon steel.

Neutral Processes Drive Seasonal Assembly of the Skin Mycobiome

The importance of microorganisms to human skin health has led to a growing interest in the temporal stability of skin microbiota. Here we investigated the dynamics and assembly of skin fungal communities (mycobiomes) with amplicon sequencing of samples collected from multiple sites on 24 healthy Chinese individuals across four seasons (in the order of winter, spring, summer, and autumn in a calendar year). We found a significant difference in community compositions between individuals, and intrapersonal community variation increased over time at all body sites. Within each season, the frequency of occurrence of most operational taxonomic units (OTUs) was well fitted by a neutral model, highlighting the importance of stochastic forces such as passive dispersal and ecological drift in skin community assembly. Despite the significant richness contributed by neutrally distributed OTUs, skin coassociation networks were dominated by taxa well-adapted to multiple body sites (forehead, forearm, and palm), although hub species were disproportionately rare. Taken together, these results suggest that while skin mycobiome assembly is a predominantly neutral process, taxa that could be under the influence of selective forces (e.g., host selection) are potentially key to the structure of a community network. IMPORTANCE Fungi are well recognized members of the human skin microbiota and are crucial to cutaneous health. Common cutaneous diseases such as seborrheic dermatitis and dermatophytes are linked to fungal species. Most studies related to skin microbial community dynamics have focused on Western subjects, while non-Western individuals are understudied. In this study, we explore the seasonal changes of the skin mycobiome in a healthy Chinese cohort and identify ecological processes that could possibly give rise to such variations. Our work reveals the dynamic nature of host skin fungal community, highlighting the dominant roles neutral forces play in the seasonal assembly of skin mycobiome. This study provides insight into the microbial ecology of the human skin microbiome and fills a knowledge gap in the literature regarding the dynamics of skin fungal community.

Resilience and Assemblage of Soil Microbiome in Response to Chemical Contamination Combined with Plant Growth

A lack of knowledge of the microbial responses to environmental change at the species and functional levels hinders our ability to understand the intrinsic mechanisms underlying the maintenance of microbial ecosystems. Here, we present results from temporal microcosms that introduced inorganic and organic contaminants into agro-soils for 90 days, with three common legume plants. Temporal dynamics and assemblage of soil microbial communities and functions in response to contamination under the influence of growth of different plants were explored via sequencing of the 16S rRNA amplicon and by shotgun metagenomics. Soil microbial alpha diversity and structure at the taxonomic and functional levels exhibited resilience patterns. Functional profiles showed greater resilience than did taxonomic ones. Different legume plants imposed stronger selection on taxonomic profiles than on functional ones. Network and random forest analyses revealed that the functional potential of soil microbial communities was fostered by various taxonomic groups. Betaproteobacteria were important predictors of key functional traits such as amino acid metabolism, nucleic acid metabolism, and hydrocarbon degradation. Our study reveals the strong resilience of the soil microbiome to chemical contamination and sensitive responses of taxonomic rather than functional profiles to selection processes induced by different legume plants. This is pivotal to develop approaches and policies for the protection of soil microbial diversity and functions in agro-ecosystems with different response strategies from global environmental drivers, such as soil contamination and plant invasion.IMPORTANCE Exploring the microbial responses to environmental disturbances is a central issue in microbial ecology. Understanding the dynamic responses of soil microbial communities to chemical contamination and the microbe-soil-plant interactions is essential for forecasting the long-term changes in soil ecosystems. Nevertheless, few studies have applied multi-omics approaches to assess the microbial responses to soil contamination and the microbe-soil-plant interactions at the taxonomic and functional levels simultaneously. Our study reveals clear succession and resilience patterns of soil microbial diversity and structure in response to chemical contamination. Different legume plants exerted stronger selection processes on taxonomic than on functional profiles in contaminated soils, which could benefit plant growth and fitness as well as foster the potential abilities of hydrocarbon degradation and metal tolerance. These results provide new insight into the resilience and assemblage of soil microbiome in response to environmental disturbances in agro-ecosystems at the species and functional levels.

Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study

Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.

Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China

BACKGROUND

The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulating bacterial abundance, diversity, and co-occurrence network. We also investigated the associations between Hg contents and the relative abundance of microbial functional genes by analyzing the soil metagenomes from a subset of those sites.

RESULTS

We found that soil Hg largely influenced the taxonomic and functional attributes of microbial communities in the two studied regions. In general, Hg pollution was negatively related to bacterial abundance, but positively related to the diversity of bacteria in two separate regions. We also found some consistent associations between soil Hg contents and the community composition of bacteria. For example, soil total Hg content was positively related to the relative abundance of Firmicutes and Bacteroidetes in both paddy and upland soils. In contrast, the methylmercury (MeHg) concentration was negatively correlated to the relative abundance of Nitrospirae in the two types of soils. Increases in soil Hg pollution correlated with drastic changes in the relative abundance of ecological clusters within the co-occurrence network of bacterial communities for the two regions. Using metagenomic data, we were also able to detect the effect of Hg pollution on multiple functional genes relevant to key soil processes such as element cycles and Hg transformations (e.g., methylation and reduction).

CONCLUSIONS

Together, our study provides solid evidence that Hg pollution has predictable and significant effects on multiple taxonomic and functional attributes including bacterial abundance, diversity, and the relative abundance of ecological clusters and functional genes. Our results suggest an increase in soil Hg pollution linked to human activities will lead to predictable shifts in the taxonomic and functional attributes in the Hg-impacted areas, with potential implications for sustainable management of agricultural ecosystems and elsewhere.

Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems

BACKGROUND

Soil microbiomes play an important role in the services and functioning of terrestrial ecosystems. However, little is known of their vertical responses to restoration process and their contributions to soil nutrient cycling in the subsurface profiles. Here, we investigated the community assembly of soil bacteria, archaea, and fungi along vertical (i.e., soil depths of 0-300 cm) and horizontal (i.e., distance from trees of 30-90 cm) profiles in a chronosequence of reforestation sites that represent over 30 years of restoration.

RESULTS

In the superficial layers (0-80 cm), bacterial and fungal diversity decreased, whereas archaeal diversity increased with increasing soil depth. As reforestation proceeded over time, the vertical spatial variation in bacterial communities decreased, while that in archaeal and fungal communities increased. Vertical distributions of the soil microbiomes were more related to the variation in soil properties, while their horizontal distributions may be driven by a gradient effect of roots extending from the tree. Bacterial and archaeal beta-diversity were strongly related to multi-nutrient cycling in the soil, respectively, playing major roles in deep and superficial layers.

CONCLUSIONS

Taken together, these results reveal a new perspective on the vertical and horizontal spatial variation in soil microbiomes at the fine scale of single trees. Distinct response patterns underpinned the contributions of soil bacteria, archaea, and fungi as a function of subsurface nutrient cycling during the reforestation of ex-arable land.

Degradation shaped bacterial and archaeal communities with predictable taxa and their association patterns in Zoige wetland at Tibet plateau

Soil microbes provide important ecosystem services. Zoige Plateau wetland, the largest alpine peat wetland in the world, has suffered from serious degradation in the past 30 years. We studied the composition of the Zoige Plateau alpine wetland soil microbiota and relations among specific taxa using 16S rRNA amplicon sequencing combined with association network analysis. Compared to the pristine swamp soil, taxons DA101, Aeromicrobium, Bradyrhizobium, and Candidatus Nitrososphaera were enriched and several methanogenic Euryarchaeota were depleted in the moderately degraded meadow soil and highly degraded sandy soil. Soil total potassium contents in soils with different degradation levels were significantly different, being the highest in meadow soil and lowest in swamp soil. The association network analysis showed that total potassium positively correlated with specific bacterial and archaeal taxa. Jiangella, Anaerolinea, Desulfobulbus, Geobacter, Flavobacterium, Methanobacterium and Methanosaeta were identified as the keystone genera in the networks. Soil degradation affected soil properties, and caused changes in the bacterial and archaeal community composition and the association patterns of community members. The changes could serve as early warning signals of soil degradation in alpine wetlands.

Distinct succession patterns of abundant and rare bacteria in temporal microcosms with pollutants

Elucidating the driving forces behind the temporal dynamics of abundant and rare microbes is essential for understanding the assembly and succession of microbial communities. Here, we explored the successional trajectories and mechanisms of abundant and rare bacteria via soil-enrichment subcultures in response to various pollutants (phenanthrene, n-octadecane, and CdCl₂) using time-series Illumina sequencing datasets. The results reveal different successional patterns of abundant and rare sub-communities in eighty pollutant-degrading consortia and two original soil samples. A temporal decrease in α-diversity and high turnover rate for β-diversity indicate that deterministic processes are the main drivers of the succession of the abundant sub-community; however, the high cumulative species richness indicates that stochastic processes drive the succession of the rare sub-community. A functional prediction showed that abundant bacteria contribute primary functions to the pollutant-degrading consortia, such as amino acid metabolism, cellular responses to stress, and hydrocarbon degradation. Meanwhile, rare bacteria contribute a substantial fraction of auxiliary functions, such as carbohydrate-active enzymes, fermentation, and homoacetogenesis, which indicates their roles as a source of functional diversity. Our study suggests that the temporal succession of microbes in polluted microcosms is mainly associated with abundant bacteria rather than the high proportion of rare taxa. The major forces (i.e., stochastic or deterministic processes) driving microbial succession could be dependent on the low- or high-abundance community members in temporal microcosms with pollutants.