Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia.

Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the 15N fixation rate by 13-fold from 0.02 to 0.28 µmol 15N2 (g dry weight soil) -1 d-1. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that Methylocystis, Methylophilaceae, and Methylomicrobium were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes (13C or 15N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that Methylocystis and Methylophilaceae had the potential to perform methane-induced BNF and likely utilized riboflavin and c-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones.

Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater.

The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.

May microbial ecological baseline exist in continental groundwater?

BACKGROUND: Microbes constitute almost the entire biological community in subsurface groundwater and play an important role in ecological evolution and global biogeochemical cycles. Ecological baseline as a fundamental reference with less human interference has been investigated in surface ecosystems such as soils, rivers, and ocean, but the existence of groundwater microbial ecological baseline (GMEB) is still an open question so far. RESULTS: Based on high-throughput sequencing information derived from national monitoring of 733 newly constructed wells, we find that bacterial communities in pristine groundwater exhibit a significant lateral diversity gradient and gradually approach the topsoil microbial latitudinal diversity gradient with decreasing burial depth of phreatic water. Among 74 phyla dominated by Proteobacteria in groundwater, Patescibacteria act as keystone taxa that harmonize microbes in shallower aquifers and accelerate decline in bacterial diversity with increasing well-depth. Decreasing habitat niche breadth with increasing well-depth suggests a general change in the relationship among key microbes from closer cooperation in shallow to stronger competition in deep groundwater. Unlike surface-water microbes, microbial communities in pristine groundwater are predominantly shaped by deterministic processes, potentially associated with nutrient sequestration under dark and anoxic environments in aquifers. CONCLUSIONS: By unveiling the biogeographic patterns and mechanisms controlling the community assembly of microbes in pristine groundwater throughout China, we firstly confirm the existence of GMEB in shallower aquifers and propose Groundwater Microbial Community Index (GMCI) to evaluate anthropogenic impact, which highlights the importance of GMEB in groundwater water security and health diagnosis. Video Abstract.

Occurrence, distribution and risk assessment of polycyclic aromatic hydrocarbons in soils around main water source areas of Beijing, China.

Polycyclic aromatic hydrocarbons (PAHs) in urban environments have been globally concerned due to their significant health impacts on residents. However, little is known about potential risks of PAHs from centralized water source areas. In the present study, 326 soils samples from the main water source areas of Beijing were collected and the occurrence, source appointment, and risks of PAHs were systematically investigated based on the monitoring results from high-performance liquid chromatography (HPLC). The total PAHs (∑16 PAHs) concentrations ranged from 5.70 to 1512 ng/g with median value of 44.2 ng/g, in which 4-ring and 5-ring groups were the major components. PAHs concentrations in the cultivated land were significantly higher than other areas, which could reflect significant impact of soil organic matter and total nitrogen contents on the spatial variations of PAHs. Further source identifications through positive matrix factorization model (PMF) revealed that biomass (22.5%), coal (21.4%), gasoline (17.6%) and diesel (16.4%) combustion were dominant sources of soil PAHs in the study area. Moreover, the risk assessment indicated that total ecological and health risk of PAHs were negligible, but individual PAH, including pyrene and benzo(b)fluoranthene, should be concerned due to their potential risks in several monitored stations located in the secondary protection area of four reservoirs. Our study provided new insights into environmental risks of soils in main water source areas from PAHs and could be helpful for organic micropollutant controlling and drinking water safety in rapidly urbanizing cities.

Distribution, source identification, and health risk of emerging organic contaminants in groundwater of Xiong'an New Area, Northern China.

Groundwater contamination in China has been greatly concerned due to dramatically increasing fresh water demand accompanied by economic development. However, little is known about aquifer vulnerability to hazardous matters especially in previously contaminated site of rapidly urbanizing cities. Here, we collected 90 groundwater samples from Xiong'an New Area during wet and dry seasons of 2019 and characterized the composition and distribution of emerging organic contaminants (EOCs) in this strategically developing city. A total of 89 EOCs, assigned to organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), and volatile organic compounds (VOCs), were detected with the frequencies ranging from 1.11 %-85.6 %. Methyl tert-butyl ether (16.3 µg/L), Epoxid A (6.15 µg/L), and α-Lindane (5.15 µg/L) could be identified as major contributors to groundwater organic pollution. Significant aggregation of groundwater EOCs along Tang River were found due to historical residue and accumulation from wastewater storage there before 2017. Significant seasonal variations (p < 0.05) in the types and concentrations of EOCs could be attributed to discrepant pollution sources between varying seasons. Human health effects from exposure to groundwater EOCs were further evaluated with negligible risk (<10-4) in most samples (97.8 %) and notable risk (10-6-10-4) in several monitored wells (2.20 %) located along Tanghe Sewage Reservoir. This study provides new evidences for aquifer vulnerability to hazardous matters in historically contaminated sites and is of significant to groundwater pollution controlling and drinking water safety for rapidly urbanizing cities.

Reactive Oxygen Species Triggered Oxidative Degradation of Polystyrene in the Gut of Superworms (Zophobas atratus Larvae).

Oxidative decomposition of polystyrene (PS) by insects has been previously demonstrated, yet little is known about the oxidation mechanism and its effect on the metabolism of plastics within the insect gut. Here, we demonstrate the generation of reactive oxygen species (ROS) in the gut of superworms (Zophobas atratus larvae) under different feeding trails, which in turn induced the oxidative decomposition of ingested PS. The ROS were commonly generated in the larva gut, and PS consumption resulted in a significant increase of ROS with a maximum ·OH of 51.2 µmol/kg, which was five times higher than in the bran feeding group. Importantly, scavenging of ROS significantly decreased the oxidative depolymerization of PS, indicating a vital role of ROS in effective PS degradation in the gut of superworms. Further investigation suggested that the oxidative depolymerization of PS was caused by the combinatorial effect of ROS and extracellular oxidases of gut microbes. These results demonstrate that ROS were extensively produced within the intestinal microenvironment of insect larvae, which greatly favored the digestion of ingested bio-refractory polymers. This work provides new insights into the underlying biochemical mechanisms of plastic degradation in the gut.

Structure, stability, and potential function of groundwater microbial community responses to permafrost degradation on varying permafrost of the Qinghai-Tibet Plateau.

The ongoing permafrost degradation under climate warming has modified aboveground biogeochemical processes mediated by microbes, yet groundwater microbial structure and function as well as their response to permafrost degradation remain poorly understood. We separately collect 20 and 22 sub-permafrost groundwater samples from Qilian Mountain (alpine and seasonal permafrost) and Southern Tibet Valley (plateau isolated permafrost) on the Qinghai-Tibet Plateau (QTP) to investigate the effects of permafrost groundwater characteristics on the diversity, structure, stability, and potential function of bacterial and fungal communities. Regional discrepancy of groundwater microbes between two permafrost regions reveals that permafrost degradation might reshape microbial community structure, increase community stability and potential functions relevant to carbon metabolism. Bacterial community assembly in permafrost groundwater is governed by deterministic processes, whereas fungal communities are mainly controlled by stochastic processes, suggesting that bacterial biomarkers might provide the better 'early warning signals' to permafrost degradation in deeper layers. Our study highlights the importance of groundwater microbes in ecological stability and carbon emission on the QTP.

Effect of metal pollution on the distribution and co-occurrence pattern of bacterial, archaeal and fungal communities throughout the soil profiles.

Metal pollution has raised negative impact on microbes, but little is known about the distribution and co-occurrence pattern of bacterial, fungal and archaeal communities along the soil profiles at multiple metal contamination sites. Here, we characterized the variations of metal concentrations and microbial communities with soil depth along five deep bores at the Tanghe Sewage Reservoir, a typical metal contamination area on the North China Plain. Co, Cd, Mg, Se, and Li were identified as the major contaminants in this area, and the pollution load index was 1.88, 1.54 and 1.62 in the shallow layer (0-0.6 m), deep layer (>2.0 m) and middle layer (0.6-2.0 m), respectively. The diversities and compositions of bacterial, archaeal and fungal communities varied significantly along the soil profiles. Deterministic process played a crucial role in shaping the difference of microbial community compositions among different soil layers, in which metal levels contributed more than soil physiochemical parameters. Furthermore, the interspecific co-occurrence network was most complex in the middle layer, indicating that metal pollution could decrease microbial network complexity. Bacterial keystone species in the co-occurrence networks showed both positive and negative correlations with polluted metals, whereas most archaeal and fungal keystone species were negatively related to multiple metals. These findings increased our understanding of distribution patterns, co-occurrence networks and environmental drivers of microbial communities in metal pollution soils.

Comammox biogeography subject to anthropogenic interferences along a high-altitude river.

The recent discovery of comammox Nitrospira performing complete ammonia oxidation to nitrate has overturned the long-held dogma of two-step nitrification on Earth, yet little is known about the effect of urbanization interference on their distribution. Using gene-centric metagenomics, we provided the first blueprints about comammox community, biogeography, and environmental drivers along a high-elevation (> 2000 m) river flowing through the largest city on the vulnerable Qinghai-Tibetan Plateau. Our study confirmed a wide presence and diversity of yet-uncultured comammox clade B across wet and dry seasons, with average 3.0 and 2.0 times as abundant as clade-A amoA genes in water and sediments, respectively. Species identified from freshwater and drinking water treatment plants dominated the comammox guilds (58∼100%), suggesting this plateau river shared a similar comammox assemblage with the above habitat types. Compared with the urban area harboring more abundant canonical Nitrospira identified in wastewater (average 24%), the upstream suburban reach had a smaller human population but larger proportions of comammox in ammonia-oxidizing prokaryotes (24∼72% of abundances) and Nitrospira sublineages I/II. Higher contents of nitrate and nitrite in water, and antibiotics in water and sediments, may restrain comammox niches in nitrifiers over the urban area. Further random forest analysis revealed that lincosamides and quinolones were the most important antibiotic predictors for the niche differentiations between comammox and canonical nitrifiers in water, while macrolides for those in sediments. Finally, by incubation experiments, we demonstrated higher activity contributions of benthic comammox in the suburban area (36.2∼92.8% of potential ammonia-oxidation rates) than in the urban reach, and that the contribution variation had significant negative relations with macrolides and their major components. Overall, this study highlighted that anthropogenic activities hampered the advantage of riverine complete nitrifiers over the canonical two-step ones.

Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau.

Microbial co-hosts of nitrate reduction genes (NRGs) and antibiotic resistance genes (ARGs) have been recently reported, but their ecology and biochemical role in urban waterways remain largely unknown. Here, we collected 29 surface water and 29 sediment samples in the Huangshui River on the Qinghai-Tibet Plateau during the wet and dry season, and 11 water samples from wastewater treatment plants and wetlands along the river. Using metagenomic sequencing, we retrieved 278 medium-to-high-quality metagenome-assembled genomes (MAGs) of NRG-ARG co-hosts, mainly belonging to the phyla Proteobacteria, Actinobacteriota, and Bacteroidota. Of microorganisms carrying ARGs, a high proportion (75.3%‒94.9%) also encoded NRGs, supporting nitrate reducing bacteria as dominant hosts of ARGs. Seasonal changes in antibiotic levels corresponded to significant variation in the relative abundance of NRG-ARG co-host in both water and sediments, resulting in a concomitant change in antibiotic resistance pathways. In contrast, the contribution of NRG-ARG co-hosts to nitrate reduction was stable between seasons. We identify specific antibiotics (e.g., sulphonamides) and microbial taxa (e.g., Acinetobacter and Hafnia) that may disproportionately impact these relationships to serve as a basis for laboratory investigations into bioremediation strategies. Our study suggests that highly abundant nitrate reducing microorganisms in contaminated environments may also directly impact human health as carriers of antibiotic resistance.

Sustained Biotic-Abiotic Hybrids Methanogenesis Enabled Using Metal-Free Black Phosphorus/Carbon Nitride.

Biotic-abiotic hybrid systems (BAHs) constructed by integrating biological methanogens with photocatalysts offer novel approaches for the effective solar-driven conversion of CO2 to CH4, providing significant inspiration for achieving carbon neutrality and alleviating the energy crisis. As metal photocatalysts would cause photocorrosion that damages microbial cells and lead to system imbalance. Therefore, exploring suitable metal-free photocatalysts is of particular importance in the search for more efficient and sustainable BAHs to improve the actual operability and applicability. Herein, black phosphorus/carbon nitride (BPCN x ) as an alternative metal-free heterostructure was combined with Methanosarcina barkeri (M. barkeri) to construct M. barkeri-BPCN x hybrid systems, and their cyclic methanogenesis performance was investigated. Our results demonstrated that BPCN x promotes the separation of photogenerated charges and enhances the quantum yield, providing a sustained energy source for the cyclically driven M. barkeri reduction of CO2 to CH4 under visible light. Our system achieved a total CH4 yield of 1087.45 ± 29.14 µmol gcat -1 after three cycles, 1.96 times higher than that of M. barkeri-Ni@CdS. M. barkeri-BPCN x overcame the defects of the metal photocatalyst and kept cell permeability, achieving cyclic stability and effectively maintaining the activity of M. barkeri. These results highlight the viable role of BPCN x as a metal-free photocatalysts in the construction of BAHs for the sustained and efficient methanation of CO2, which is conducive to the development of an environmentally-friendly, low-cost, and efficient strategy for the conversion of CO2 to CH4.

Multiple metal(loid) contamination reshaped the structure and function of soil archaeal community.

Archaea are important participants in biogeochemical cycles of metal(loid)-polluted ecosystems, whereas archaeal structure and function in response to metal(loid) contamination remain poorly understood. Here, the effects of multiple metal(loid) pollution on the structure and function of archaeal communities were investigated in three zones within an abandoned sewage reservoir. We found that the high-contamination zone (Zone I) had higher archaeal diversity but a lower habitat niche breadth, relative to the mid-contamination zone (Zone II) and low-contamination zone (Zone III). Particularly, metal-resistant species represented by potential methanogens were markedly enriched in Zone I (cumulative relative abundance: 32.24%) compared to Zone II (1.93%) and Zone III (0.10%), and closer inter-taxon connections and higher network complexity (based on node number, edge number, and degree) were also observed compared to other zones. Meanwhile, the higher abundances of potential metal-resistant and methanogenic functions in Zone I (0.24% and 9.24%, respectively) than in Zone II (0.08% and 7.52%) and Zone III (0.01% and 1.03%) suggested archaeal functional adaptation to complex metal(loid) contamination. More importantly, six bioavailable metal(loid)s (titanium, tin, nickel, chromium, cobalt, and zinc) were the main contributors to archaeal community variations, and metal(loid) pollution reinforced the role of deterministic processes, particularly homogeneous selection, in the archaeal community assembly. Overall, this study provides the first integrated insight into the survival strategies of archaeal communities under multiple metal(loid) contamination, which will be of significant guidance for future bioremediation and environmental governance of metal(loid)-contaminated environments.

Different spatiotemporal dynamics, ecological drivers and assembly processes of bacterial, archaeal and fungal communities in brackish-saline groundwater.

The presence of brackish-saline groundwater (BSG) poses great harms for human health, agricultural and industrial activity. Understanding how the major environmental features in BSG determine microbiota coalescence is crucial for groundwater monitoring optimization. Based on metabarcoding analysis of 242 PCR-amplified samples, we provided the first blueprints about distinct spatiotemporal distributions, ecological drivers and assembly processes of bacterial, archaeal and fungal communities in BSG obtained from new-constructed wells at Xiong'an New Area, China. Our study demonstrated that bacterial and archaeal communities exhibited significant spatial turnovers, while fungal community displayed the most obvious seasonal variation. Environmental filtering drove bacterial compositions more than those of archaea and fungi. Total dissolved solids (TDS), one of the most critical hydrochemical factors for salinization, had a stronger effect on bacterial spatiotemporal turnover than on those of the other two taxonomic groups, while chemical oxygen demand (CODMn) was more significantly associated with prokaryotic community variations. Bacterial and archaeal taxa dominated the metacommunity network and connected closely, and TDS was mostly related to archaeal subnetwork topological features, suggesting a significant influence of TDS on species association patterns within archaea. Specific functional guilds like bacterial nitrite oxidation, anammox, and archaeal methanogenesis were enriched in lower-TDS habitats, while higher TDS favored bacterial communities involved in dark oxidation of sulfur compounds, fumarate respiration, and cellulolysis. Finally, we confirmed that bacterial and archaeal assembly processes were governed by determinism in each season, and that of fungi was more regulated by stochasticity. Higher TDS was speculated to lead bacterial assembly more deterministic and that of fungi more random. Together, these findings provided an integrate theoretical framework about the unique responses of the three life domains to brackish-saline stress, and had important implications for microbial ecological prediction in groundwater.

Spatiotemporal distribution, risk assessment and source appointment of metal(loid)s in water and sediments of Danjiangkou Reservoir, China.

Danjiangkou Reservoir is the biggest artificial reservoir in China. But spatiotemporal distribution and risks of metal(loid)s in it were still unclear after the operation of Middle Route of South-to-North Water Diversion Project. In this study, distribution pattern of fifteen metal(loid)s in the Danjiangkou Reservoir was investigated. It was shown that metal(loid)s concentrations in the water were much lower than the drinking water quality standards in China, while Sb, Co, Cd and Cr were identified as the major pollutants in the sediments. Environment-metal(loid)s correlation analysis revealed total organic carbon, sulfate, temperature, dissolved oxygen and total phosphorus markedly controlled metal(loid)s distribution in the water, while organic carbon, total phosphorus and ammonia nitrogen shaped their distribution in the sediments. Results of risk assessment further revealed that the sediments of Danjiangkou Reservoir were minor to moderate polluted, and Sb, Cd exhibited the highest potential ecological risk. Additionally, source identification showed agricultural activities (25.3%), industrial and mining activities (17.5%) and natural processes (57.2%) were the dominant sources of metal(loid)s burden in the sediments. Overall, the results are of significance to understanding the ecological risk and pollution sources in the Danjiangkou Reservoir, which is essential for the effective management of metal(loid)s pollution.