Natural organic small molecules promote the aging of plastic wastes and refractory carbon decomposition in water

Microplastics and nanoplastics are ubiquitous in rivers and undergo environmental aging. However, the molecular mechanisms of plastic aging and the in-depth effects of aging on ecological functions remain unclear in waters. The synergies of microplastics and nanoplastics (polystyrene as an example) with natural organic small molecules (e.g., natural hyaluronic acid and vitamin C related to biological tissue decomposition) are the key to producing radicals (•OH and •C). The radicals promote the formation of bubbles on plastic surfaces and generate derivatives of plastics such as monomer and dimer styrene. Nanoplastics are easier to age than microplastics. Pristine plastics inhibit the microbial Shannon diversity index and evenness, but the opposite results are observed for aging plastics. Pristine plastics curb pectin decomposition (an indicator of plant-originated refractory carbon), but aging plastics promote pectin decomposition. Microplastics and nanoplastics undergoing aging processes enhance the carbon biogeochemical cycle. For example, the increased carbohydrate active enzyme diversity, especially the related glycoside hydrolase and functional species Pseudomonas and Clostridium, contributes to refractory carbon decomposition. Different from the well-studied toxicity and aging of plastic pollutants, this study connects plastic pollutants with biological tissue decomposition, biodiversity and climate change together in rivers.

Impact of waste separation on the biological nitrogen removal in a MSW incineration leachate treatment plant: Performance and microbial community shift

After waste separation program was launched in China in 2019, incineration leachate treatment plants are facing a challenge of effective removal of nitrogen from leachate due to lack of sufficient carbon source. In this study, the performance of a biological incineration leachate treatment process (anaerobic digestion (AD) - two-stage anoxic/aerobic (A/O) process) was evaluated after adopting the waste separation program, and the changes in the microbial community and function was analyzed using 16S rRNA amplicon sequencing technology. Results showed that after the waste separation, the influent chemical oxygen demand (COD) concentration reduced by 90% (from 19,300 to 1780 mg L-1) with the COD/N ratio decreased from 12.3 to 1.4, which led to a decreased nitrogen removal efficiency (NRE) of <65% and a high effluent NO3- accumulation (445.8-986.5 mg N·L-1). By bypassing approximately 60% of the influent to the two-stage A/O process and adding external carbon source (glucose), the mean NRE increased to 86.3 ± 7.4%. Spearman's analysis revealed that refractory compounds in the bypassed leachate were closely related to the variations in bacterial community composition and nitrogen removal function in the two-stage A/O, leading to a weakened correlation of microbial network. KEGG functional pathway predictions based on Tax4Fun also confirmed that the bypassed leachate induced xenobiotic compounds to the two-stage A/O process, the relative abundance of nitrogen metabolism was reduced by 32%, and more external carbon source was required to ensure the satisfactory nitrogen removal of >80%. The findings provide a good guide for regulation of incineration leachate treatment processes after the waste separation.

Differences in greenhouse gas emissions and microbial communities between underground and conventionally constructed wastewater treatment plants

Large quantities of greenhouse gases (GHGs) are emitted into the atmosphere during wastewater treatment. In this study, GHG and microbial samples were collected from four wastewater treatment plants (WWTPs), and their differences and relationships were assessed. The study showed that, compared with conventionally constructed WWTPs, well-established gas collection systems in underground WWTPs facilitate comprehensive collection and accurate accounting of GHGs. In aboveground WWTPs, capped anoxic ponds promote methane production releasing it at 2-8 times the rate of uncapped emissions, in contrast to nitrous oxide emissions. Moreover, a stable subsurface environment allows for smaller fluctuations in daily GHG emissions and higher microbial diversity and abundance. This study highlights differences in GHG emission fluxes and microbial communities in differently constructed WWTPs, which are useful for control and accurate accounting of GHG emissions.

Metals and microorganisms in a Maar lake sediment core indicating the anthropogenic impact over last 800 years

A closed Maar lake, receiving mostly atmospheric deposition, offers a unique setting for investigating the impact of human activities on the environment. In this study, we aimed to investigate the historical record of metals in core sediments of Maar Lake in Huguangyan (HGY), Southeast China, and elucidate the possible microbial responses to anthropogenic metal stress. Five stages were divided according to the historical record of metals and corresponding distribution of microbial community, among which Pb and Sn showed a peak value around 1760 CE, indicating the ancient mining and smelting activities. Since the 1980s, a substantial enrichment of metals such as Zn, As, Mo, Cd, Sn, Sb, and Pb was observed, due to the rapid industrial growth in China. In terms of microorganisms, Chloroflexi phylum, particularly dominated by Anaerolineales, showed significant correlations with Pb and Sn, and could potentially serve as indicator species for mining and smelting-related contamination. Desulfarculales and Desulfobacterales were found to be more prevalent in recent period and exhibited positive correlations with anthropogenic metals. Moreover, according to the multivariate regression modeling and variance decomposition analysis, Pb and Sn could regulate Anaerolineales and further pose impact on the carbon cycle; while sulfate-reducing bacteria (SRB) could response to anthropogenic metals and influence sulfur cycle. These findings provide new insights into the interaction between metals and microbial communities over human history.

Toxicity factors to assess the ecological risk for soil microbial communities

The toxicity factor (TF), a critical parameter within the potential ecological risk index (RI), is determined without accounting for microbial factors. It is considerable uncertainty exists concerning its validity for quantitatively assessing the influence of metal(loid)s on microorganisms. To evaluate the suitability of TF, we constructed microcosm experiments with varying RI levels (RI = 100, 200, 300, 500, and 700) by externally adding zinc (Zn), chromium (Cr), copper (Cu), lead (Pb), nickel (Ni), cadmium (Cd), and mercury (Hg) to uncontaminated soil (CK). Quantitative real-time PCR (qPCR) and high-throughput sequencing techniques were employed to measure the abundance and community of bacteria and fungi, and high-throughput qPCR was utilised to quantify functional genes associated with CNPS cycles. The results demonstrated that microbial diversity and function exhibited significant alterations (p < 0.05) in response to increasing RI levels, and the influences on microbial community structure, enzyme activity, and functional gene abundances were different due to the types of metal(loid)s treatments. At the same RI level, significant differences (p < 0.05) were discerned in microbial diversity and function across metal(loid) treatments, and these differences became more pronounced (p < 0.001) at higher levels. These findings suggest that TF may not be suitable for the quantitative assessment of microbial ecological risk. Therefore, we adjusted the TF by following three steps (1) determining the adjustment criteria, (2) deriving the initial TF, and (3) adjusting and optimizing the TF. Ultimately, the optimal adjusted TF was established as Zn = 1.5, Cr = 4.5, Cu = 6, Pb = 4.5, Ni = 5, Cd = 22, and Hg = 34. Our results provide a new reference for quantitatively assessing the ecological risks caused by metal(loid)s to microorganisms.

The distinct phases of fresh-seawater mixing intricately regulate the nitrogen transformation processes in a high run-off estuary: Insight from multi-isotopes and microbial function analysis

Excessive anthropogenic nitrogen inputs lead to the accumulation of nitrogen, and significantly impact the nitrogen transformation processes in estuaries. However, the governing of nitrogen during its transport from terrestrial to estuary under the influence of diverse human activities and hydrodynamic environments, particularly in the fresh-seawater mixing zone, remains insufficient researched and lack of basis. To address this gap, we employed multi-isotopes, including δ15N-NO3-, δ18O-NO3-, δ15N-NH4+, and δ15N-PN, as well as microbial function analysis, to investigate the nitrogen transformation processes in the Pearl River Estuary (PRE), a highly anthropogenic and terrestrial estuary. Principle component analysis (PCA) confirmed that the PRE could clearly partitioned into three zone, e.g., terrestrial area (T zone), mixing area (M zone) and seawater area (S zone), in terms of nitrogen transportation and transformation processes. The δ15N-NO3- (3.38±0.60‰) and δ18O-NO3- (6.35±2.45‰) results in the inner estuary (T area) indicate that NO3-attributed to the domestic sewage and groundwater discharge in the river outlets lead to a higher nitrification rate in the outlets of the Pearl River than in the reaching and seawater intrusion areas, although nitrate is rapidly diluted by seawater after entering the estuary. The transformation of nitrogen in the T zone was under significant nitrogen fixation (0.61 ± 0.22 %) and nitrification processes (0.0043 ± 0.0032 %) (presumably driven by Exiguobacterium sp. (14.1 %) and Cyanobium_PCC-6307 (8.1 %)). In contrast, relatively low δ15N-NO3- (6.83 ± 1.24‰) and high δ18O-NO3- (22.13±6.01‰) imply that atmospheric deposition has increased its contribution to seawater nitrate and denitrification (0.53±0.13 %) was enhanced by phytoplankton/bacterial (such as Psychrobacter sp. and Rhodococcus) in the S zone. The assimilation of NH4 results from the ammonification of NO3- reduces δ15N-NH4+ (5.36 ± 1.49‰) and is then absorbed by particulate nitrogen (PN). The retention of nitrogen when fresh-seawater mixing enhances the elevation of δ15N-NH4+ (8.19 ± 2.19‰) and assimilation of NH4+, leading to an increase in PN and δ15N-PN (6.91 ± 1.52‰) from biological biomass (mainly Psychrobacter sp. and Rhodococcus). The results of this research demonstrate a clear and comprehensive characterization of the nitrogen transformation process in an anthropogenic dominated estuary, highlighting its importance for regulating the nitrogen dissipation in the fresh-seawater mixing process in estuarine ecosystems.

Characteristics variations of size-fractionated anammox granules and identification of the potential effects on these evolutions

Anaerobic ammonium oxidation (anammox) granulation which contributed to system stabilization and performance improvement has great potential in the field of wastewater nitrogen removal. The researchers fractionated anammox granules into small-size (0.5-0.9 mm), medium-size (1.8-2.2 mm), and large-size (2.8-3.5 mm) categories to examine their properties and mechanisms. Various analyses, including high-throughput sequencing, determination of inorganic elements and extracellular polymeric substances (EPS), and microbial function prediction, were conducted to characterize these granules and understand their impact. The results revealed distinct characteristics among the different-sized granules. Medium-size granules exhibited the highest sphericity, EPS content, and anammox abundance. In contrast, large-size granules had the highest specific surface area, heme c content, specific anammox activity, biodiversity, and abundance of filamentous bacteria. Furthermore, the precipitates within the granules were identified as CaCO3 and MgCO3, with the highest inorganic element content found in the large-size granules. Microbial community and function annotation also varied with granule size. Based on systematic analysis, the researchers concluded that cell growth, chemical precipitation, EPS secretion, and interspecies interaction all played a role in granulation. Small-size granules were primarily formed through cell growth and biofilm formation. As granule size increased, EPS secretion and chemical precipitation became more influential in the granulation process. In the large-size granules, chemical precipitation and interspecies interaction, including synergistic effects with nitrifying, denitrifying, and filamentous bacteria, as well as metabolic cross-feeding, played significant roles in aggregation. This interplay ultimately contributed to higher anammox activity in the large-size granules. By fully understanding the mechanisms involved in granulation, this study provides valuable insights for the acclimation of anammox granules with optimal sizes under different operational conditions.

Soil microbial community composition and functions are disrupted by fire and land use in a Mediterranean woodland

The intersection of fire, land use transformations, and climate change is putting Mediterranean climate-type ecosystems at risk of soil degradation and loss of ecosystem services. Ondik et al. (2022b) showed that in a Mediterranean dry sclerophyll woodland of South Australia, high severity fire and clearing and grazing practices impacted both physicochemical and biological soil quality indicators. Building upon the work of Ondik et al. (2022b) this study aims to 1) identify soil physicochemical properties impacted by fire and land management that are indirect drivers of changes to soil microbial community composition and 2) determine whether the observed changes to soil microbial community composition affect soil microbial functions. Via a redundancy analysis, we identified fire and management-induced changes to pH, soil water repellency, nutrient stoichiometry, and total nutrient content as significant drivers of the composition of soil microbial communities. We then measured basal respiration, substrate induced respiration, and the carbon mineralisation quotient, and calculated functional trait distributions among microbial communities by linking 16S and 18S rRNA sequences to respiration modes and functional guilds, respectively. We found that fire reduced soil microbial respiration and the relative abundance (RA) of microbial symbionts, anaerobic bacteria, and microaerophilic bacteria, while increasing the RA of aerobic bacteria. Furthermore, management increased the RA of post-fire ectomycorrhizal fungi and may have reduced pathogenic load, microbial efficiency, and wood saprotrophs, while increasing litter, soil, and other saprotrophic species that are adapted to grasslands. This study shows that, through changes to microbial community composition, high severity wildfire and land management affected soil respiration rates, bacterial modes of respiration, prevalence of symbiotic bacteria and fungi, and microbial substrate preference. Having identified the main physicochemical drivers of changes to microbial community composition, we provide valuable insights into how fire and land management can impact soils in Mediterranean woodland.

Effects of complex pollution by microplastics and heavy metals on soil physicochemical properties and microbial communities under alternate wetting and drying conditions

Microplastics (MPs) broadly coexist with heavy metals (HMs) in soil, Cd and Cu are the main types of soil HMs contamination, in addition to polystyrene (PS), which is also widely present in the environment and prone to aging. However, differences in the effects of MPs and HMs on soil properties and microbial characteristics under alternating wetting and drying (AWD) remain unclear. Thus, this study investigated the effects of four conventional (0.2% (w/w)) and aged MPs in indoor incubation experiments on soil properties under desiccation (Dry) and AWD. We found that with the influence of the "enzyme lock" theory, the coexistence of MPs and HMs under Dry had a more pronounced effect on soil physicochemical properties, whereas the effects on soil enzyme activity under AWD were more significant. In addition, MPs decreased the available Cu by 4.27% and, conversely, increased the available Cd by 8.55%. Under Dry, MPs affected microbial function mainly through physicochemical properties, with a contribution of approximately 72.4%, whereas under AWD enzyme activity and HMs were significantly greater, with increases of 28.2% and 7.9%, respectively. These results indicate that the effects of MPs on environmental variation and microbial profiles under AWD conditions differed significantly from those under Dry.

Responses of the structure and function of microbes in Yellow River Estuary sediments to different levels of mercury

The health and stability of the estuary of the Yellow River ecosystem have come under increasing pressure from land-based inputs of heavy metals. While it is known that heavy metals affect the function and health of the microbial community, there remains little knowledge on the responses of the microbial community to heavy metals, particularly highly toxic mercury. The research aimed to characterize the responses of the sediment microbial community of the estuary of the Yellow River to different levels of mercury stress. Estuary sediment samples were collected for microbial community analysis, measurement of mercury [including total mercury (THg) and methylmercury (MeHg)], and measurement of other physicochemical factors, including pH, total organic carbon (TOC), sulfide, iron ratio (Fe3+/Fe2+), ammonium salt (NH4+), and biochemical oxygen demand (BOD). The application of 16S rRNA sequencing identified 60 phyla of bacteria, dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Stations with higher THg or MeHg and lower microbial abundance and diversity were generally distributed further outside of the estuary. Besides mercury, the measured physicochemical factors had impacts on microbial diversities and distribution. Metagenomics assessment of three stations, representative of low, moderate, and high mercury concentrations and measured physicochemical factors, revealed the abundances and functions of predicted genes. The most abundant genes regulating the metabolic pathways were categorized as metabolic, environmental information processing, and genetic information processing, genes. At stations with high levels of mercury, the dominant genes were related to energy metabolism, signal transport, and membrane transport. Functional genes with a mercury-resistance function were generally in the mer system (merA, merC, merT, merR), alkylmercury lyase, and metal-transporting ATPase. These results offer insight into the microbial community structure of the sediments in the Yellow River Estuary and the microbial function of mercury resistance under mercury stress.

Effect of lactic acid bacteria on the structure and potential function of the microbial community of Nongxiangxing Daqu

OBJECTIVES

The microbial community structure of the saccharifying starter, Nongxiangxing Daqu(Daqu), is a crucial factor in determining Baijiu's quality. Lactic acid bacteria (LAB), are the dominant microorganisms in the Daqu. The present study investigated the effects of LAB on the microbial community structure and its contribution to microbial community function during the fermentation of Daqu.

METHODS

The effect of LAB on the structure and function of the microbial community of Daqu was investigated using high-throughput sequencing technology combined with multivariate statistical analysis.

RESULTS

LAB showed a significant stage-specific evolution pattern during Daqu fermentation. The LEfSe analysis and the random forest learning algorithm identified LAB as vital differential microorganisms during Daqu fermentation. The correlation co-occurrence network showed aggregation of LAB and Daqu microorganisms, indicating LAB's significant position in influencing the microbial community structure, and suggests that LAB showed negative correlations with Bacillus, Saccharopolyspora, and Thermoactinomyces but positive correlations with Issatchenkia, Candida, Acetobacter, and Gluconobacter. The predicted genes of LAB enriched 20 functional pathways during Daqu fermentation, including Biosynthesis of amino acids, Alanine, aspartate and glutamate metabolism, Valine, leucine and isoleucine biosynthesis and Starch and sucrose metabolism, which suggested that LAB had the functions of polysaccharide metabolism and amino acid biosynthesis.

CONCLUSION

LAB are important in determining the composition and function of Daqu microorganisms, and LAB are closely related to the production of nitrogenous flavor substances in Daqu. The study provides a foundation for further exploring the function of LAB and the regulation of Daqu quality.

Inorganic amendments improve acidic paddy soils: Effects on soil properties, Al fractions, and microbial communities

Alkaline soil inorganic amendments (SIAs) have been extensively used to improve acidic soils. In this study, we arranged 9 treatments of low, medium, and high application dosages of silicon calcium magnesium potassium fertilizer, calcium magnesium phosphate fertilizer, and lime in the field to study the mechanism of SIAs in improving acidic soils. The Al sequential extraction experiment showed that the application of SIAs tended to transform from active to stable fractions of Al. By amplicon sequencing, it was observed that the application of SIAs significantly affected microbial community compositions in rhizosphere soils. With the decrease in soil acidity, the microbial function was also enhanced, especially the activity of dehydrogenase. In this study, the acidity-related indicators in soils (pH, exchangeable acid, and exchangeable base cations) were first integrated into an index-AIV (acidity improvement value), which was used to assess the relationship with other soil properties. The redundancy analysis and correlation network between soil chemical and biological indexes indicated that SIAs did not greatly affect the fungi community structure, while greatly increased or decreased the abundance of bacteria, especially Acidobacteria, Nitrospirae, and Crenarchaeota. Our data revealed the SIAs optimized soil environment for rice growth jointly by decreasing Al mobility, improving soil microbial function, and increasing soil fertility.

Synergistic mechanisms of bioorganic fertilizer and AMF driving rhizosphere bacterial community to improve phytoremediation efficiency of multiple HMs-contaminated saline soil

The addition of Arbuscular mycorrhizal fungi (AMF) or bioorganic fertilizer (BOF) alone has been reported to enhance plant tolerance to heavy metals and salt stress and promote plant growth, while their synergistic effects on plant growth and rhizosphere microorganism are largely unknown. This study explored the effects of AMF (Rhizophagus intraradices), BOF and BOF + RI assisted phytoremediation on heavy metals contaminated saline soil improvement and revealed the microbial mechanism. For this purpose, a pot trial consisting of four treatments (CK, RI, BOF and BOF + RI) was carried out. The results showed that the biomass, nutrient element contents, the accumulation of heavy metals and Na of Astragalus adsurgens and soil properties were most significantly improved by BOF + RI. BOF + RI significantly impacted rhizosphere microbial diversity, abundance and community composition. Chloroflexi and Patescibacteria at the phylum level and Actinomadura, Iamia, and Desulfosporosinus at the genus level were significantly enriched in BOF + RI. Network analysis revealed that BOF + RI significantly changed the keystone and enhanced complexity and interaction. Most of the keystones had roles in promoting plant growth and stress resistance. This study suggested that phytoremediation assisted by BOF and AMF is an attractive approach to ameliorate heavy metals contaminated saline soil.

Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia

Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.

Microbial taxonomic and functional shifts in adolescents with type 1 diabetes are associated with clinical and dietary factors

BACKGROUND

Evidence indicates a link between the pathogenesis of type 1 diabetes (T1D) and the gut microbiome. However, the regulation of microbial metabolic pathways and the associations of bacterial species with dietary factors in T1D are largely unknown. We investigated whether microbial metagenomic signatures in adolescents with T1D are associated with clinical/dietary factors.

METHODS

Adolescents with T1D (case) and healthy adolescents (control) were recruited, and microbiome profiling in participants' stool samples was performed using shotgun metagenomic sequencing. The bioBakery3 pipeline (Kneaddata, Metaphlan 4 and HUMAnN) was used to assign taxonomy and functional annotations. Clinical (HbA1c) and dietary information (3-day food record) were collected for conducting association analysis using Spearman's correlation.

FINDINGS

Adolescents with T1D exhibited modest changes in taxonomic composition of gut microbiome. Nineteen microbial metabolic pathways were altered in T1D, including downregulation of biosynthesis of vitamins (B2/flavin, B7/biotin and B9/folate), enzyme cofactors (NAD⁺ and s-adenosyl methionine) and amino acids (aspartate, asparagine and lysine) with an upregulation in the fermentation pathways. Furthermore, bacterial species associated with dietary and clinical factors differed between healthy adolescents and adolescents with T1D. Supervised models modeling identified taxa predictive of T1D status, and the top features included Coprococcus and Streptococcus.

INTERPRETATION

Our study provides new insight into the alteration of microbial and metabolic signatures in adolescents with T1D, suggesting that microbial biosynthesis of vitamins, enzyme cofactors and amino acids may be potentially altered in T1D.

FUNDING

Research grants from NIH/NCCIH: R01AT010247 and USDA/NIFA: 2019-67017-29253; and Larry & Gail Miller Family Foundation Assistantship.

Understory ferns promote the restoration of soil microbial diversity and function in previously degraded lands

Microorganisms facilitate the recovery of previously degraded soils, such as degraded lands experiencing vegetation restoration and understory expansion, through vital soil functions like nutrient cycling and decomposing organic matter. Despite the role of microorganisms in recovery, little is known about the effects of the process on microbial diversity and function. Here, we performed an understory fern, Dicranopteris dichotoma (Thunb.) Berhn removal treatments nested within three Masson pine (Pinus massoniana L.) plantations with different restoration years in subtropical China. Three ferns treatments including no ferns cover, with ferns cover, and the ferns removal treatments were established to assess the impact of the ferns on soil microbial diversity and function during revegetation and drivers of observed changes. We combined high-throughput sequencing, network structure modeling, and function prediction of soil bacterial and fungal communities to determine microbial diversity and functions. Our results showed that soil bacterial and fungal diversity increased with restoration time. Understory ferns significantly increased soil microbial diversity in the un-restored land but the effect became smaller in two restored sites. Understory ferns significantly increased the relative abundance of bacterial phyla Proteobacteria and Acidobacteria, but decreased that of Chloroflexi and Firmicutes. Furthermore, the presence of ferns increased the abundance of Basidiomycota, but increased the abundance of Ascomycota. Co-occurrence network analysis revealed that the presence of ferns leads to more complex of bacterial networks with more connections, nodes, average degrees, betweenness, and degrees. The functional predictions indicate that aerobic chemoheterotrophy, chemoheterotrophy, and nitrogen fixation functional groups play key roles in the nutrient cycling of soils with ferns cover. The bacterial and fungal community compositions were strongly affected by revegetation and understory ferns as litter biomass and soil nitrogen were identified as the key environmental factors. Our study highlights the role of understory in facilitating microbial diversity and function recovery during degraded lands restoration.

Bioorganic fertilizers improve the adaptability and remediation efficiency of Puccinellia distans in multiple heavy metals-contaminated saline soil by regulating the soil microbial community

Soil salinization and heavy metal (HM) pollution are global environmental problems. Bioorganic fertilizers facilitate phytoremediation, but their roles and microbial mechanisms in natural HM-contaminated saline soils have not been explored. Therefore, greenhouse pot trials were conducted with three treatments: control (CK), manure bioorganic fertilizer (MOF), and lignite bioorganic fertilizer (LOF). The results showed that MOF and LOF significantly increased nutrient uptake, biomass, toxic ion accumulation in Puccinellia distans, soil available nutrients, SOC, and macroaggregates. More biomarkers were enriched in MOF and LOF. Network analysis confirmed that MOF and LOF increased the number of bacterial functional groups and fungal community stability and strengthened their positive association with plants; Bacteria have a more significant effect on phytoremediation. Most biomarkers and keystones play important roles in promoting plant growth and stress resistance in the MOF and LOF treatments. In summary, besides enrichment of soil nutrients, MOF and LOF can also improve the adaptability and phytoremediation efficiency of P. distans by regulating the soil microbial community, with LOF having a greater effect.

Spatiotemporal Dynamics of Bacterial Taxonomic and Functional Profiles in Estuarine Intertidal Soils of China Coastal Zone

Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats.

Leveraging microbiome rediversification for the ecological rescue of soil function

BACKGROUND

Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples.

RESULTS

Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions.

CONCLUSIONS

In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.

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.

Metagenomic analysis and nitrogen removal performance evaluation of activated sludge from a sequencing batch reactor under different salinities

The effect of salinity on the nitrogen removal performance and microbial community of activated sludge was investigated in a sequencing batch reactor. The NH₄⁺-N removal efficiency was over 95% at 0-4% salinity, indicating that the nitrification performance of activated sludge was slightly affected by lower salinity. The obvious nitrite accumulation was observed with the increment of the salinity to 5%, followed by a notable decline in the nitrogen removal performance at 6% salinity. The salinity inhibited the microbial activity, and the specific rate of nitrification and denitrification was decreased by the increasing salinity obviously. Additionally, the lower activity of superoxide dismutase and peroxidase and higher reactive oxygen species content in activated sludge might account for the deteriorative nitrogen removal performance at 6% salinity. Metagenomics analysis revealed that the genes encoding the ABC-type quaternary amine transporter in the ABC transporter pathway were abundant in the activated sludge at 2% and 4% salinity, and the higher salinity of 6% led to the loss of the genes encoding the p-type Na⁺ transporter in the ABC transporter pathway. These results indicated that the salinity could weaken the ABC transporter pathway for the balance of osmotic pressure in activated sludge. The microbial activity and nitrogen removal performance of activated sludge were decreased due to the unbalanced osmotic pressure at higher salinity.

Consistency between the metabolic performance of two aerobic granular sludge systems and the functional groups of bacteria detected by amplicon sequencing

Two sequential batch reactors (R1 and R2) of aerobic granular sludge (AGS) were inoculated with activated sludge of different origins. The objective was to investigate the granulation and the consistency between the structure of the microbial communities (16S rRNA amplicon sequencing) in each reactor and their metabolic performance (removal of C, N, and P). Both reactors were fed with acetate-based synthetic wastewater, targeting an anaerobic-aerobic cycle reputed to favor the phosphorus- and glycogen-accumulating organisms (PAO and GAO). Stable granulation was achieved in both reactors, where, instead of PAO, the dominant genera were ordinary heterotrophic organisms (OHO) such as Thauera, Paracoccus, and Flavobacterium known for their high capacity of aerobic storage of polyhydroxyalkanoates (PHA). Generally, there was good consistency between the metabolic behavior of each reactor and the bacterial genera detected. Both reactors showed high removals of C and complete nitrification (Nitrosomonas and Nitrospira detected) but a low level of simultaneous nitrification-denitrification (SND) during the aerated phase. The latter causes that nitrates were recycled to the initial phase, in detriment of PAO selection. Meanwhile, the study showed that selecting slow-growing OHOs (with aerobic storage capacity) favors stable granulation, revealing an alternative AGS technology for C and N removal.

Elevated O3 Exerts Stronger Effects than Elevated CO2 on the Functional Guilds of Fungi, but Collectively Increase the Structural Complexity of Fungi in a Paddy Soil

Global climate change is characterized by altered global atmospheric composition, including elevated CO₂ and O₃, with important consequences on soil fungal communities. However, the function and community composition of soil fungi in response to elevated CO₂ together with elevated O₃ in paddy soils remain largely unknown. Here we used twelve open-top chamber facilities (OTCs) to evaluate the interactive effect of CO₂ (+ 200 ppm) and O₃ (+ 40 ppb) on the diversity, gene abundance, community structure, and functional composition of soil fungi during the growing seasons of two rice cultivars (Japonica, Wuyujing 3 vs. Nangeng 5055) in a Chinese paddy soil. Elevated CO₂ and O₃ showed no individual or combined effect on the gene abundance or relative abundance of soil fungi, but increased structural complexity of soil fungal communities, indicating that elevated CO₂ and/or O₃ promoted the competition of species-species interactions. When averaged both cultivars, elevated CO₂ showed no individual effect on the diversity or abundance of functional guilds of soil fungi. By contrast, elevated O₃ significantly reduced the relative abundance and diversity of symbiotrophic fungi by an average of 47.2% and 39.1%, respectively. Notably, elevated O₃ exerts stronger effects on the functional processes of fungal communities than elevated CO₂. The structural equation model revealed that elevated CO₂ and/or O₃ indirectly affected the functional composition of soil fungi through community structure and diversity of soil fungi. Root C/N and soil environmental parameters were identified as the top direct predictors for the community structure of soil fungi. Furthermore, significant correlations were identified between saprotrophic fungi and root biomass, symbiotrophic fungi and root carbon, the pathotroph-symbiotroph and soil pH, as well as pathotroph-saprotroph-symbiotroph and soil microbial biomass carbon. These results suggest that climatic factors substantially affected the functional processes of soil fungal, and threatened soil function and food production, highlighting the detrimental impacts of high O₃ on the function composition of soil biota.

A sustainable approach for bioremediation of secondary salinized soils: Studying remediation efficiency and soil nitrate transformation by bioaugmentation

Nitrate is the main nitrogen source for plant growth, but it can also pollute the environment. A major cause of soil secondary salinization is the rising level of nitrates in the soil, which poses a threat to the sustainability and fertility of global greenhouse soils. Herein, Bacillus megaterium NCT-2 was used as a microbial agent to remove nitrate by bioaugmentation, and the remediation efficiency of secondary salinized soil in different degrees was evaluated. The findings showed that the highest nitrate removal rate of 62.76% was in a medium degree of secondary salinized soil. Moreover, the results of 16S rRNA high-throughput sequencing and quantitative real-time PCR (qPCR) demonstrated that NCT-2 agent reduced the microbial diversity, increased the microbial community stability, and changed the composition and function of the microbial community were changed by NCT-2 agent in all districts soil. Further analysis demonstrated that the NCT-2 bacterial agent significantly increased the key enzyme genes of the assimilation pathway (nitrite reductase gene NasD, 87-404 times, and glutamine reduction enzyme gene GlnA, 13-52 times) and dissimilatory reduction to ammonium (DNRA) (nitrate reductase gene NarG, 14-56 times) in different degrees of secondary salinized soils. This proved that NCT-2 agent could promote the nitrate assimilation and the dissimilation and reduction to ammonium in secondary salinized soil. Thus, the current findings suggested that the NCT-2 agent has a significant potential for reducing excessive nitrate levels in secondary salinized soil. The remediation efficiency was related to the microbial community composition and the degree of secondary salinization. This study could provide a theoretical basis for the remediation of secondary salinized soil in the future.

Enhanced removal of antibiotics and antibiotic resistance genes in a soil microbial fuel cell via in situ remediation of agricultural soils with multiple antibiotics

Soil microbial fuel cells (MFCs) have been applied for the in situ remediation of soils polluted by single antibiotics. However, the investigation of only single antibiotic pollution has hindered MFC application in real-world soil remediation, where the effects of multiple antibiotics with similar chemical structures on the fate of antibiotics and their corresponding antibiotic resistance genes (ARGs) remain unknown. In this study, antibiotic removal rates, microbial community compositions, metabolite compositions, and ARG abundances were investigated in soil MFCs by adding two commonly used antibiotics (sulfadiazine, SDZ, and sulfamethoxazole, SMX), and comparing them with the addition of only a single antibiotic (SDZ). The antibiotic removal rate was higher in the soil MFC with addition of mixed antibiotics compared to the single antibiotic due to enhanced biodegradation efficiency in both the upper (57.24% of the initial antibiotic concentration) and lower layers (57.07% of the initial concentration) of the antibiotic-polluted soils. Bacterial community diversity in the mixed antibiotic conditions increased, and this likely resulted from the decreased toxicity of intermediates produced during antibiotic biodegradation. Moreover, the addition of mixed antibiotics led to lower risks of ARG release into soil environments, as reflected by higher abundances of host bacteria in the single antibiotic treatment. These results encourage the further development of soil MFC technology for in situ remediation of antibiotic-polluted soils.