Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics

Quorum sensing-enhanced electron transfer in anammox consortia: A mechanism for improved resistance to variable-valence heavy metals

Quorum sensing (QS) is recognized for enhancing bacterial resistance against heavy metals by regulating the production of extracellular substances that hinder metal penetration into the intracellular environment. However, it remains unclear whether QS contributes to resistance by regulating electron transfer, thereby transforming metals from more toxic to less toxic forms. This study investigated the regulatory mechanism of acyl-homoserine lactone (AHL)-mediated QS on electron transfer under As(III) and Cr(VI) stress. Metagenomic binning results revealed that Candidatus Brocadia sinica serves as a major contributor to AHL production for regulating heavy metal resistance, while other symbiotic bacteria offer complementary resistance pathways. In these bacteria, the AHL synthesis gene htdS plays a pivotal role in QS regulation of electron transfer and heavy metal resistance. Experimental findings demonstrated that AHL increased the electron transport system activity by 19.8 %, and upregulated electron transfer gene expression by 1.1- to 6.9-fold. The enhanced electron transfer facilitated a 28.7 % increase in the transformation of As(III) to less toxic As(V) and monomethylarsonic acid, ultimately achieving efficient nitrogen removal under As(III) stress. This study expands our understanding of how QS strengthens bacterial resistance to heavy metals, offering novel strategies for enhancing nitrogen removal of anammox in heavy metal-contaminated environments.

An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov

The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.

Metabolic diversity and adaptation of carbon-fixing microorganisms in extreme glacial cryoconite

Understanding the diversity and functionality of carbon-fixing microorganisms in glacial ecosystems is crucial for elucidating carbon cycling processes in extreme environments. This study investigates the composition, diversity, and metabolic potential of carbon-fixing microorganisms in Tibetan cryoconite. Through metagenomic sequencing, we identified 13 carbon-fixing metagenome-assembled genomes spanning ten known and three unclassified genera. Deoxyribonucleic acid -stable isotope probing experiments with 13C-labeled sodium bicarbonate confirmed the metabolic activity of key genera, including Cyanobacteria (Microcoleus and Phormidesmis) and Proteobacteria (Rhizobacter and Rhodoferax). Our results reveal a diverse array of carbon fixation pathways, with the Calvin-Benson-Bassham cycle and 3-hydroxypropionate bicycle being the most prominent. In addition to photoautotrophic microorganisms, chemoautotrophic microorganisms also contribute to carbon fixation through mechanisms such as sulfur oxidation and atmospheric reducing gas utilization. The study highlights the adaptability of microbial communities to varying environmental conditions, including fluctuations in oxygen, light, and substrate availability. The findings underscore the complex interplay between carbon fixation pathways and environmental factors in cryoconite ecosystems. It also emphasizes the importance of exploring alternative carbon fixation pathways to gain a more comprehensive understanding of carbon cycling in these harsh and dynamic ecosystems.

Metagenomic analysis of the dichotomous role of uranium in regulating intracellular and extracellular antibiotic resistance genes in activated sludge

Antibiotic resistance genes (ARGs) in activated sludge include intracellular ARGs (iARGs) and extracellular ARGs (eARGs), both of which are recognized as emerging pollutants. While the activated sludge process has been commonly considered for treating wastewater contaminated with radionuclide, the effects and mechanisms of radioactive heavy metals on the fate of iARGs and eARGs (i/e-ARGs) in activated sludge are largely elusive. Here, the distribution, mobility, and hosts of i/e-ARGs in activated sludge during environmental concentrations (50 μg/L and 5000 μg/L) of radioactive uranium (U) stress were explored via metagenomics. The results revealed that the total relative abundance of iARGs and eARGs decreased by 11.62% and 10.41%, respectively, after 90 days of 50 μg/L of U treatment. In contrast, both i/e-multi- and tetracycline ARGs remarkably increased after being exposed to 5000 μg/L of U. Additionally, exposure to 5000 μg/L of U triggered notable decrease in i/e-insertion sequences and plasmids abundance, but significantly enriched i/e-integrons (p < 0.05). Partial least squares pathway modelling indicated that the prevalence of iARGs and eARGs in activated sludge was primarily driven by bacterial hosts and functional genes, respectively. Our findings revealed the dichotomous variation landscape and mechanisms of i/e-ARGs dynamics in activated sludge during U exposure, offering valuable insights for controlling ARGs risk during radioactive wastewater treatment.

Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils

The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.

A bacteria-based index of biotic integrity indicates aquatic ecosystem restoration

Intensive ecological interventions have been carried out in highly polluted shallow lakes to improve their environments and restore their ecosystems. However, certain treatments, such as dredging polluted sediment and stocking fish, can impact the aquatic communities, including benthos and fishes. These impacts can alter the composition and characteristics of aquatic communities, which makes community-based ecological assessments challenging. Here we develop a bacteria-based index of biotic integrity (IBI) that can clearly indicate the restoration of aquatic ecosystems with minimal artificial interventions. We applied this method to a restored shallow lake during 3-year intensive ecological interventions. The interventions reduced nutrients and heavy metals by 27.1% and 16.7% in the sediment, while the total organic carbon (TOC) increased by 8.0% due to the proliferation of macrophytes. Additionally, the abundance of sulfur-related metabolic pathways decreased by 10.5% as the responses to improved ecosystem. The score of bacteria-based IBI, which is calculated based on the diversity, composition, and function of benthic bacterial communities, increased from 0.62 in 2018 to 0.81 in 2021. Our study not only provides an applicable method for aquatic ecological assessment under intensive artificial interventions but also extends the application of IBI to complex application scenarios, such as ecosystems with significantly different aquatic communities and comparisons between different basins.

Weak magnetic field promotes denitrification by stimulating ferromagnetic ion-containing metalloprotein expression

Weak magnetic field (WMF) has been recognized to promote biological denitrification processes; however, the underlying mechanisms remain largely unexplored, hindering the optimization of its effectiveness. Here, we systematically investigated the effects of WMF on denitrification performance, enzyme activity, microbial community, and metaproteome in packed bed bioreactors treating high nitrate wastewater under different WMF intensities and C:N ratios. Results showed that WMFs significantly promoted denitrification by consistently stimulating the activities of denitrifying reductases and NAD+/NADH biosynthesis across decreasing C:N ratios. Reductases and electron transfer enzymes involved in denitrification were overproduced due to the significantly enriched overexpression of ferromagnetic ion-containing (FIC) metalloproteins. We also observed WMFs' intensity-dependent selective pressure on microbial community structures despite the effects being limited compared to those caused by changing C:N ratios. By coupling genome-centric metaproteomics and structure prediction, we found the dominant denitrifier, Halomonas, was outcompeted by Pseudomonas and Azoarcus under WMFs, likely due to its structural deficiencies in iron uptake, suggesting that advantageous ferromagnetic ion acquisition capacity was necessary to satisfy the substrate demand for FIC metalloprotein overproduction. This study advances our understanding of the biomagnetic effects in the context of complex communities and highlights WMF's potential for manipulating FIC protein-associated metabolism and fine-tuning community structure.

Structural and functional bacterial biodiversity in a copper, zinc and nickel amended bioreactor: shotgun metagenomic study

BACKGROUND

At lower concentrations copper (Cu), zinc (Zn) and nickel (Ni) are trace metals essential for some bacterial enzymes. At higher concentrations they might alter and inhibit microbial functioning in a bioreactor treating wastewater. We investigated the effect of incremental concentrations of Cu, Zn and Ni on the bacterial community structure and their metabolic functions by shotgun metagenomics. Metal concentrations reported in previous studies to inhibit bacterial metabolism were investigated.

RESULTS

At 31.5 μM Cu, 112.4 μM Ni and 122.3 μM Zn, the most abundant bacteria were Achromobacter and Agrobacterium. When the metal concentration increased 2 or fivefold their abundance decreased and members of Delftia, Stenotrophomonas and Sphingomonas dominated. Although the heterotrophic metabolic functions based on the gene profile was not affected when the metal concentration increased, changes in the sulfur biogeochemical cycle were detected. Despite the large variations in the bacterial community structure when concentrations of Cu, Zn and Ni increased in the bioreactor, functional changes in carbon metabolism were small.

CONCLUSIONS

Community richness and diversity replacement indexes decreased significantly with increased metal concentration. Delftia antagonized Pseudomonas and members of Xanthomonadaceae. The relative abundance of most bacterial genes remained unchanged despite a five-fold increase in the metal concentration, but that of some EPS genes required for exopolysaccharide synthesis, and those related to the reduction of nitrite to nitrous oxide decreased which may alter the bioreactor functioning.

A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies

Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.

Metaproteomics-informed stoichiometric modeling reveals the responses of wetland microbial communities to oxygen and sulfate exposure

Climate changes significantly impact greenhouse gas emissions from wetland soil. Specifically, wetland soil may be exposed to oxygen (O2) during droughts, or to sulfate (SO42-) as a result of sea level rise. How these stressors - separately and together - impact microbial food webs driving carbon cycling in the wetlands is still not understood. To investigate this, we integrated geochemical analysis, proteogenomics, and stoichiometric modeling to characterize the impact of elevated SO42- and O2 levels on microbial methane (CH4) and carbon dioxide (CO2) emissions. The results uncovered the adaptive responses of this community to changes in SO42- and O2 availability and identified altered microbial guilds and metabolic processes driving CH4 and CO2 emissions. Elevated SO42- reduced CH4 emissions, with hydrogenotrophic methanogenesis more suppressed than acetoclastic. Elevated O2 shifted the greenhouse gas emissions from CH4 to CO2. The metabolic effects of combined SO42- and O2 exposures on CH4 and CO2 emissions were similar to those of O2 exposure alone. The reduction in CH4 emission by increased SO42- and O2 was much greater than the concomitant increase in CO2 emission. Thus, greater SO42- and O2 exposure in wetlands is expected to reduce the aggregate warming effect of CH4 and CO2. Metaproteomics and stoichiometric modeling revealed a unique subnetwork involving carbon metabolism that converts lactate and SO42- to produce acetate, H2S, and CO2 when SO42- is elevated under oxic conditions. This study provides greater quantitative resolution of key metabolic processes necessary for the prediction of CH4 and CO2 emissions from wetlands under future climate scenarios.

[Microbial metaproteomics--From sample processing to data acquisition and analysis]

Microorganisms are closely associated with human diseases and health. Understanding the composition and function of microbial communities requires extensive research. Metaproteomics has recently become an important method for throughout and in-depth study of microorganisms. However, major challenges in terms of sample processing, mass spectrometric data acquisition, and data analysis limit the development of metaproteomics owing to the complexity and high heterogeneity of microbial community samples. In metaproteomic analysis, optimizing the preprocessing method for different types of samples and adopting different microbial isolation, enrichment, extraction, and lysis schemes are often necessary. Similar to those for single-species proteomics, the mass spectrometric data acquisition modes for metaproteomics include data-dependent acquisition (DDA) and data-independent acquisition (DIA). DIA can collect comprehensive peptide information from a sample and holds great potential for future development. However, data analysis for DIA is challenged by the complexity of metaproteome samples, which hinders the deeper coverage of metaproteomes. The most important step in data analysis is the construction of a protein sequence database. The size and completeness of the database strongly influence not only the number of identifications, but also analyses at the species and functional levels. The current gold standard for metaproteome database construction is the metagenomic sequencing-based protein sequence database. A public database-filtering method based on an iterative database search has been proven to have strong practical value. The peptide-centric DIA data analysis method is a mainstream data analysis strategy. The development of deep learning and artificial intelligence will greatly promote the accuracy, coverage, and speed of metaproteomic analysis. In terms of downstream bioinformatics analysis, a series of annotation tools that can perform species annotation at the protein, peptide, and gene levels has been developed in recent years to determine the composition of microbial communities. The functional analysis of microbial communities is a unique feature of metaproteomics compared with other omics approaches. Metaproteomics has become an important component of the multi-omics analysis of microbial communities, and has great development potential in terms of depth of coverage, sensitivity of detection, and completeness of data analysis.

Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity

Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.

Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes

Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4+, NO2- and SO42, while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.

Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater

Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.

Toxic effects of nanoplastics on biological nitrogen removal in constructed wetlands: Evidence from iron utilization and metabolism

Nanoplastics (NPs) in wastewaters may present a potential threat to biological nitrogen removal in constructed wetlands (CWs). Iron ions are pivotal in microbially mediated nitrogen metabolism, however, explicit evidence demonstrating the impact of NPs on nitrogen removal regulated by iron utilization and metabolism remains unclear. Here, we investigated how NPs disturb intracellular iron homeostasis, consequently interfering with the coupling mechanism between iron utilization and nitrogen metabolism in CWs. Results indicated that microorganisms affected by NPs developed a siderophore-mediated iron acquisition mechanism to compensate for iron loss. This deficiency resulted from NPs internalization limited the activity of the electron transport system and key enzymes involved in nitrogen metabolism. Microbial network analysis further suggested that NPs exposure could potentially trigger destabilization in microbial networks and impair effective microbial communication, and ultimately inhibit nitrogen metabolism. These adverse effects, accompanied by the dominance of Fe3+ over certain electron acceptors engaged in nitrogen metabolism under NPs exposure, were potentially responsible for the observed significant deterioration in nitrogen removal (decreased by 30 %). This study sheds light on the potential impact of NPs on intracellular iron utilization and offers a substantial understanding of the iron-nitrogen coupling mechanisms in CWs.

Critical steps in an environmental metaproteomics workflow

Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.

Effect and potential mechanisms of sludge-derived chromium, nickel, and lead on soil nitrification: Implications for sustainable land utilization of digested sludge

Increasing occurrence of heavy metals (HMs) in sewage sludge threatens its widespread land utilization in China due to its potential impact on nutrient cycling in soil, requiring a better understanding of HM-induced impacts on nitrification. Herein, lab-scale experiments were conducted over 185-day, evaluating the effect of sludge-derived chromium (Cr3+), nickel (Ni2+), and lead (Pb2+) on soil nitrification at different concentrations. Quantitative polymerase chain reaction and linear regression results revealed an inhibitory sequence of gene abundance by HMs' labile fraction: ammonia-oxidizing bacteria (AOB)-ammonia monooxygenase (amoA)> nitrite oxidoreductase subunit alpha (nxrA)> nitrite oxidoreductase subunit beta (nxrB). The toxicity of HMs' incremental labile fraction decreased in the order of Ni2+>Cr3+>Pb2+, with respective threshold values of 5.01, 24.03 and 38.42 mg·kg-1. Furthermore, extending incubation time reduced HMs inhibition on ammonia oxidation, mainly related to their fraction bound to carbonate minerals. Random Forest analysis, variation partitioning analysis, and Mantel test indicated that soil physicochemical properties primarily affected nitrification genes, especially in the test of Cr3+ on AOB-amoA, nxrA, nxrB, Ni2+ for complete ammonia-oxidizing bacteria-amoA, and Pb2+ for nxrA and nxrB. These findings underline the importance of labile HMs fractions and soil physicochemical properties to nitrification, guiding the establishment of HM control standards for sludge utilization.

High geogenic soil thallium shows limited impact on bacterial community

Thallium (Tl) is a highly toxic trace metal, included in the US EPA list of priority pollutants. Even though its toxicity is potentially higher or comparable to Cd or Hg, its environmental impact is largely unknown. Despite its toxicity, only a few recent studies are mapping the impact of recently introduced Tl on soil microbial communities, namely in agricultural systems but no studies focus on its long term effect. To complement the understanding of the impact of Tl on soil, this study aims to describe the influence of extremely high naturally occurring Tl concentration (50 mg/kg of potentially bioavailable Tl) on soil microbial communities. Our investigation concentrated on samples collected at Buus (Erzmatt, Swiss Jura, Switzerland), encompassing forest and meadow soil profiles of the local soil formed on hydrothermally mineralized dolomite rock, which is naturally rich in Tl. The soil profiles showed a significant proportion of potentially bioavailable Tl. Yet, even this high concentration of Tl has a limited impact on the richness of the soil bacterial community. Only the meadow soil samples show a reduced richness compared to control samples. Furthermore, our analysis of geogenic Tl contamination in the region unveiled a surprising finding: compared to other soils of Switzerland and in stark contrast to soils affected by recent mining activities, the structure of the bacterial community in Buus remained relatively unaffected. This observation highlights the unique ability of soil microbial communities to withstand extreme Tl contamination. Our study advances the understanding of Tl's environmental impact and underscores the resilience of soil microbes in the face of severe long-term contamination.

Novel α-amino acid-like structure decorated biochar for heavy metal remediation in acid soil

Neither chemical nor physical adsorption play well in heavy metals remediation in acid soil due to the competing behavior of abundant protons, where stable chelators that can be reused are of significant demand. Herein, biochar with abundant nitro and carboxyl groups is prepared, which can be assembled into self-supporting electrode. Under the catalyzation of electricity, the surface decorated -NO2 on the biochar can be in situ transformed into -NH2. Combined with the carboxyl group that attached on the same carbon atom, a special α-amino acid-like structure modified biochar (α-AC@BC) can be successfully constructed. Due to the strong affinity between the α-amino acid-like ligand and heavy metals, this α-AC@BC exhibits high removal efficiencies of 83.41%, 80.94%, 92.54% and 77.05% for available copper, cadmium, lead and zinc respectively, even in a strong acid soil with low pH of 4. After four adsorption-desorption cycles, the α-AC@BC could still eliminate 83.88% of copper. The high adsorption energy among -NH2, -COOH and heavy metals (-2.99 eV for copper, -1.90 eV for lead, -1.30 eV for zinc and -0.91 eV for cadmium) could form steady coordination structure to guarantee a highly practical application potential of α-AC@BC in strong acid soil. This study provides a novel concept for the decontamination of multiple heavy metal polluted acid soil.

Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome

The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.

Elucidating the roles of Cr(VI)-Cu(II) Co-pollution in the stress of aniline degradation stress: Insights into metabolic pathways and functional genes

In order to examine the impact of Cu(II)-Cr(VI) co-pollution in printing and dyeing wastewater on the aniline biodegradation system (ABS), loading experiments were conducted on ABS at varying concentrations of Cu(II)-Cr(VI). The synergistic stress imposed by Cu(II)-Cr(VI) accelerated the deterioration of the systems, with only the C2-3 (2 mg/L Cr(VI)-3 mg/L Cu(II)) sustaining stable operation for 42 days. However, its nitrogen removal performance remained significantly impaired, resulting in a total nitrogen (TN) removal rate below 40%. High-throughput sequencing analysis revealed a stronger correlation between Cr(VI) and microbial diversity compared to Cu(II). Metagenomic sequencing results demonstrated that Cu(II) emerged as the dominant factor influencing the distribution of dominant bacteria in C2-3, as well as its contribution to contaminant degradation. The complex co-pollution systems hindered aniline degradation and nitrogen metabolism through the combined bio-toxicity of heavy metals and aniline, thereby disrupting the transport chain within the systems matrix.

Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils

Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.

Heavy metal effects on multitrophic level microbial communities and insights for ecological restoration of an abandoned electroplating factory site

The response of soil microbes to heavy metal pollution provides a metric to evaluate the soil health and ecological risks associated with heavy metal contamination. However, a multitrophic level perspective of how soil microbial communities and their functions respond to long-term exposure of multiple heavy metals remains unclear. Herein, we examined variations in soil microbial (including protists and bacteria) diversity, functional guilds and interactions along a pronounced metal pollution gradient in a field surrounding an abandoned electroplating factory. Given the stressful soil environment resulting from extremely high heavy metal concentrations and low nutrients, beta diversity of protist increased, but that of bacteria decreased, at high versus low pollution sites. Additionally, the bacteria community showed low functional diversity and redundancy at the highly polluted sites. We further identified indicative genus and "generalists" in response to heavy metal pollution. Predatory protists in Cercozoa were the most sensitive protist taxa with respect to heavy metal pollution, whereas photosynthetic protists showed a tolerance for metal pollution and nutrient deficiency. The complexity of ecological networks increased, but the communication among the modules disappeared with increasing metal pollution levels. Subnetworks of tolerant bacteria displaying functional versatility (Blastococcus, Agromyces and Opitutus) and photosynthetic protists (microalgae) became more complex with increasing metal pollution levels, indicating their potential for use in bioremediation and restoration of abandoned industrial sites contaminated by heavy metals.

Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei

Lacticaseibacillus paracasei is an economically important bacterial species, used in the food industry and as a probiotic. Here, we investigate the roles of N6-methyladenine (6mA) modification in L. paracasei using multi-omics and high-throughput chromosome conformation capture (Hi-C) analyses. The distribution of 6mA-modified sites varies across the genomes of 28 strains, and appears to be enriched near genes involved in carbohydrate metabolism. A pglX mutant, defective in 6mA modification, shows transcriptomic alterations but only modest changes in growth and genomic spatial organization.

Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring

The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.

Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations

Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.

Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars

Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.

Structural and functional characteristics of soil microbial communities in response to different ecological risk levels of heavy metals

Objective

The potential ecological risk index (RI) is the most commonly used method to assess heavy metals (HMs) contamination in soils. However, studies have focused on the response of soil microorganisms to different concentrations, whereas little is known about the responses of the microbial community structures and functions to HMs at different RI levels.

Methods

Here, we conducted soil microcosms with low (L), medium (M) and high (H) RI levels, depending on the Pb and Cd concentrations, were conducted. The original soil was used as the control (CK). High-throughput sequencing, qPCR, and Biolog plate approaches were applied to investigate the microbial community structures, abundance, diversity, metabolic capacity, functional genes, and community assembly processes.

Result

The abundance and alpha diversity indices for the bacteria at different RI levels were significantly lower than those of the CK. Meanwhile, the abundance and ACE index for the fungi increased significantly with RI levels. Acidobacteria, Basidiomycota and Planctomycetes were enriched as the RI level increased. Keystone taxa and co-occurrence pattern analysis showed that rare taxa play a vital role in the stability and function of the microbial community at different RI levels. Network analysis indicates that not only did the complexity and vulnerability of microbial community decrease as risk levels increased, but that the lowest number of keystone taxa was found at the H level. However, the microbial community showed enhanced intraspecific cooperation to adapt to the HMs stress. The Biolog plate data suggested that the average well color development (AWCD) reduced significantly with RI levels in bacteria, whereas the fungal AWCD was dramatically reduced only at the H level. The functional diversity indices and gene abundance for the microorganisms at the H level were significantly lower than those the CK. In addition, microbial community assembly tended to be more stochastic with an increase in RI levels.

Conclusion

Our results provide new insight into the ecological impacts of HMs on the soil microbiome at different risk levels, and will aid in future risk assessments for Pb and Cd contamination.

Comparing with oxygen, nitrate simplifies microbial community assembly and improves function as an electron acceptor in wastewater treatment

Biochemical oxidation and reduction are key processes in treating biological wastewater and they require the presence of electron acceptors. The functional impact of electron acceptors on microbiomes provides strategies for improving the treatment efficiency. This research focused on two of the most important electron acceptors, nitrate and oxygen. Molecule ecological network, null model, and functional prediction based on high-throughput sequencing were used to analyze the microbiomes features and assembly mechanism. The results revealed nitrate via the homogeneous selection (74.0%) decreased species diversity, while oxygen via the homogeneous selection (51.1%) and dispersal limitation (29.6%) increased the complexity of community structure. Microbes that were more strongly homogeneously selected for assembly included polyphosphate accumulating organisms (PAOs), such as Pseudomonas and variovorax in the nitrate impacted community; Pseudomonas, Candidatus_Accumulibacter, Thermomonas and Dechloromonas, in the oxygen impacted community. Nitrate simplified species interaction and increased the abundance of functional genes involving in tricarboxylic acid cycle (TCA cycle), electron transfer, nitrogen metabolism, and membrane transport. These findings contribute to our knowledge of assembly process and interactions among microorganisms and lay a theoretical basis for future microbial regulation strategies in wastewater treatment.

Potentiality of phosphorus-accumulating organisms biomasses in biosorption of Cd(II), Pb(II), Cu(II) and Zn(II) from aqueous solutions: Behaviors and mechanisms

Heavy metal pollution is consistently a critical global issue, and bioremediation is regarded as one of the most promising approaches. In this work, the biosorption characteristics of Cd(II), Pb(II), Cu(II) and Zn(II) from aqueous solutions using three phosphorus-accumulating organisms (PAOs) biomasses, Ochrobactrum cicero (PAB-006), Stenotrophomonas maltophilia (PAB-009), and Pseudomonas putida (PAB-0031), as biosorbents were investigated. Results indicated that the equilibrium biosorption capacities of biosorbents to heavy metal ions were sensitive to the solution pH, and increased with increasing pH values. The experimental data of Cd(II), Pb(II), Cu(II) and Zn(II) biosorption were in good agreement with the Pseudo-second-order, Redlich-Peterson and Temkin models, implying that the biosorption was a hybrid chemical reaction-biosorption process. In addition, the theoretical maximum biosorption capacities of Cd(II), Pb(II), Cu(II) and Zn(II) were calculated to be 67.84, 80.23, 50.56 and 63.07 mg/g for PAB-006, 59.99, 87.71, 39.26 and 64.00 mg/g for PAB-009 and 68.31, 85.43, 38.97 and 62.85 mg/g for PAB-031, respectively (pH = 5.0 ± 0.1, T = 25 °C), according to the parameters of the Langmuir model. Moreover, ionic strength had negligible influences or slight promoting effects, while humic acid exhibited positive effects on the removal of heavy metals. Further, PABs were stable and displayed excellent reusability. Characterization techniques of FTIR and XPS revealed that surface complexation, ion exchange, hydrogen bonding and electrostatic interaction were the main mechanisms involved in the biosorption process. In summary, the biosorbent PABs possessed high biosorption performance with excellent reusability, and which hold the great application prospect in the treatment of heavy metal contaminated water.

Bacterial community response to chronic heavy metal contamination in marine sediments of the East China Sea

Marine sediments act as a sink for various heavy metals, which may have profound impact on sedimentary microbiota. However, our knowledge about the collaborative response of bacterial community to chronic heavy metal contamination remains little. In this study, concentrations of seven heavy metals (As, Cd, Cr, Cu, Hg, Pb, and Zn) in sediments collected from the East China Sea were analyzed and Illumina Miseq 16 S rRNA sequencing was applied to characterize the structure of bacterial community. Microbiota inhabiting sediments in the East China Sea polluted with heavy metals showed different community composition from relatively pristine sites. The response of bacterial community to heavy metal stress was further interrogated with weighted correlation network analysis (WGCNA). WGCNA revealed ten bacterial modules exhibiting distinct co-occurrence patterns and among them, five modules were related to heavy metal pollution. Three of them were positively correlated with an increase in at least one heavy metal concentration, hubs (more influential bacterial taxa) of which were previously reported to be involved in the geochemical cycling of heavy metals or possess tolerance to heavy metals, while another two modules showed opposite patterns. Our research suggested that ecological functional transition might have occurred in East China Sea sediments by shifts of community composition with sensitive modules majorly involved in the meaningful global biogeochemical cycling of carbon, sulfur, and nitrogen replaced by more tolerant groups of bacteria due to long-term exposure to low-concentration heavy metals. Hubs may serve as indicators of perturbations of benthic bacterial community caused by heavy metal pollution and support monitoring remediation of polluted sites in marine environments.

Unraveling diverse survival strategies of microorganisms to vanadium stress in aquatic environments

Worldwide vanadium contamination is posing serious risks to ecosystems. Although abilities of microbial communities to cope with vanadium stress using specific survival strategies have been reported, little is known regarding their relative importance and the underlying detoxification/tolerance mechanisms. Herein, we investigated the potential survival strategies of microbial communities and associated pathways in aquatic environments based on geochemistry and molecular biology. High vanadium content was observed for both water (12.6 ± 1.15 mg/L) and sediment (1.18 × 10³ ± 10.4 mg/kg) in the investigated polluted stream. Co-occurrence network investigation implied that microbial communities showed cooperative interactions to adapt to the vanadium-polluted condition. Vanadium was also characterized as one of the vital factors shaping the community structure via redundancy analysis and structural equation models. Based on the metagenomic technology, three survival strategies including denitrification pathway, electron transfer, and metal resistance in innate microbes under the vanadium stress were revealed, with comprehensively summarized vanadium detoxification/tolerance genes. Remarkable role of electron transfer genes and the prevalent existence of resistance genes during detoxifying vanadium were highlighted. Overall, these findings provide novel insights into survival strategies under the vanadium contamination in aquatic environments, which can be of great significance for the identification, isolation, and application of vanadium reducing bacteria in vanadium bioremediation.

AHLS-pred: a novel sequence-based predictor of acyl-homoserine-lactone synthases using machine learning algorithms

Acyl-homoserine-lactones (AHLs), as the major quorum sensing (QS) signalling molecules in Gram-negative bacteria, have shown great application potential in regulating biological nutrient removal process. The identification of AHLs synthases plays an essential role in in-depth research on QS mechanisms and applications of biological wastewater treatment processes. This work proposed the first prediction model for AHLs synthases based on machine learning algorithms, namely, AHLS-pred. The training dataset AHLS1400 and the independent testing dataset AHLS132 for AHLSs prediction were first established. Three sequence-based feature extraction methods are utilized to generate feature descriptors, namely, amino acid composition, dipeptide composition and G-gap dipeptide composition respectively. Subsequently, the optimal features were obtained based on the sorted feature descriptors (in F-score order) and the sequential forward search strategy. By comparing five different machine learning algorithms, the final prediction model is trained with support vector machine classifier on AHLS1400 in fivefold cross-validation with the best performance (ACC = 99.43%, MCC = 0.989, AUC = 0.997). The results show that AHLS-pred achieves an ACC of 94.70%, MCC of 0.894 and AUC of 0.995 on the independent testing dataset AHLS132. It demonstrates that AHLS-pred is a promising and powerful prediction method for accelerating the process of AHLSs computational identification.

Comparison of bacterial communities and their functional profiling using 16S rRNA gene sequencing between the inherent serpentine-associated sites, hyper-accumulator, downgradient agricultural farmlands, and distal non-serpentine soils

This study aims to determine and compare the bacterial community and functional profiles associated with serpentine sites, innate hyper-accumulating weed, downgradient agricultural farmlands and non-serpentine sites using 16S rRNA gene sequencing. Elemental analysis revealed that the serpentine rock and weathered soil have higher magnesium, nickel, chromium, magnesium/calcium and lower calcium/magnesium ratios and agricultural farmlands have recorded elevated chromium. Proteobacteria were found predominant, except the non-serpentine site which was rich in Cyanobacteria. PCA analysis at the genus level indicates the uniqueness of different experimental groups, except the hyperaccumulators which exhibited relatively less dissimilarity. The shift analysis showed the serpentine sites were characterized by the abundance of bacteria having heavy metal effluxion. The hyper-accumulating weeds were higher in plant growth-promoting bacteria expressing tolerance against heavy metals toxicity such as nickel, chromium, cobalt and arsenic. Besides, the agricultural lands were abundant in wetland-associated methanogens and metal (manganese, iron and zinc) transporting function related bacteria. The results suggest that the inherent edaphic factors including heavy metal content, the interacting behavior of hyperaccumulator's rhizosphere microbiota with soil and anthropogenic activities such as agricultural practices could be a major determinant of the variation in the bacterial community selection and abundance in the respective study sites.

Interactions between antibiotics and heavy metals determine their combined toxicity to Synechocystis sp

Co-pollution of antibiotics and metals is prevailing in aquatic environments. However, risks of coexisted antibiotics and metals on aquatic organisms is unclear. This study investigated the combined toxicity of antibiotics and metals towards Synechocystis sp. PCC 6803, a cyanobacterium. We found that the joint toxicity of antibiotics and metals is dependent on their interplays. The complexation between chlortetracycline (CTC) and copper/cadmium (Cu(II)/Cd(II)) resulted in their antagonistic toxicity. Contrarily, an additive toxicity was found between florfenicol (FLO) and Cu(II)/Cd(II) due to lack of interactions between them. CTC facilitated the intracellular uptake of Cu(II) and Cd(II) by increasing the membrane permeability. However, FLO had no obvious effects on the internalization of metals in Synechocystis sp. Proteomic analysis revealed that the photosynthetic proteins was down-regulated by CTC and FLO, and ribosome was the primary target of FLO. These results were verified by parallel reaction monitoring (PRM). Cu(II) induced the up-regulation of iron-sulfur assembly, while Cd(II) disturbed the cyclic electron transport in Synechocystis sp. The co-exposure of CTC and metals markedly alleviated the dysregulation of proteins, while the co-exposure of FLO and metals down-regulated biological functions such as ATP synthesis, photosynthesis, and carbon fixation of Synechocystis sp., compared with their individuals. This supports their joint toxicity effects. Our findings provide better understanding of combined toxicity between multiple pollutants in aquatic environments.

Coexistence of silver ion and tetracycline at environmentally relevant concentrations greatly enhanced antibiotic resistance gene development in activated sludge bioreactor

Antibiotic resistance has become a global public health problem. Recently, various environmental pollutants have been reported to induce the proliferation of antibiotic resistance. However, the impact of multiple pollutants (e.g., heavy metals and antibiotics), which more frequently occur in practical environments, is poorly understood. Herein, one widely distributed heavy metal (Ag⁺) and one frequently detected antibiotic (tetracycline) were chosen to investigate their coexisting effect on the proliferation of antibiotic resistance in the activated sludge system. Results show that the co-occurrence of Ag⁺ and tetracycline at environmentally relevant concentrations exhibited no distinct inhibition in reactor performances. However, they inhibited the respiratory activity by 42%, destroyed the membrane structure by 218%, and increased membrane permeability by 29% compared with the blank control bioreactor. Moreover, the relative abundances of target antibiotic resistance genes (ARGs) (e.g., tetA, bla_TEM-1, and sulII) in effluent after exposure of coexisting Ag⁺ and tetracycline were increased by 92-1983% compared with those in control reactor, which were 1.1-4.3 folds higher than the sum of the sole ones. These were possibly attributed to the enrichments of antibiotic-resistant bacteria. The results would illumine the coexisting effect of heavy metals and antibiotics on the dissemination of ARGs in activated sludge system.

Ecological Insights Into Community Interactions, Assembly Processes and Function in the Denitrifying Phosphorus Removal Activated Sludge Driven by Phosphorus Sources

The microbial characteristics in the wastewater treatment plants (WWTPs) strongly affect their optimal performance and functional stability. However, a cognitive gap remains regarding the characteristics of the microbial community driven by phosphorus sources, especially co-occurrence patterns and community assembly based on phylogenetic group. In this study, 59 denitrifying phosphorus removal (DPR) activated sludge samples were cultivated with phosphorus sources. The results suggested that homogeneous selection accounted for the largest proportion that ranged from 35.82 to 64.48%. Deterministic processes dominated in 12 microbial groups (bins): Candidatus_Accumulibacter and Pseudomonas in these bins belonged to phosphate-accumulating organisms (PAOs). Network analysis revealed that species interactions were intensive in cyclic nucleoside phosphate-influenced microbiota. Function prediction indicated that cyclic nucleoside phosphates increased the activity of enzymes related to denitrification and phosphorus metabolism and increased the α-diversity of microorganism but decreased the diversity of metabolic function. Based on these results, it was assumed that cyclic nucleoside phosphates, rather than inorganic phosphates, are the most available phosphorus source for majority microorganisms in DPR activated sludge. The study revealed the important role of phosphorus source in the construction and assembly of microbial communities and provided new insights about pollutant removal from WWTPs.

Insight into the effects of regulating denitrification on composting: Strategies to simultaneously reduce environmental pollution risk and promote aromatic humic substance formation

Denitrification during composting is a hidden danger that causes environmental pollution risk and aromatic humic substance damage, which needs to be better regulate urgently. In this study, two denitrification regulation methods, moisture and biochar amendment, were conducted during chicken manure composting. Denitrification performance data showed two regulation methods obviously reduced NO₃^--N, NO₂^--N and N₂ contents. Humic substance increased by 25.3 % and 29.1 % under two regulations. Microbiological analysis indicated that two regulation methods could decreasing denitrifying functional microbes with aroma degradation capability. Subsequently, denitrification gene narG, nirS, nosZ were significantly inhibited (p < 0.05) and the aromatic degradation metabolism pathways were down-regulated. Correlation analysis further revealed the important influence of interspecific interactions and non-biological characteristics on functional microbes. These results provided important scientific basis to denitrification regulation in the practice of composting, which achieved the purpose of simultaneously controlling environmental pollution risk and conducing end-product formation.

Nitrate shifted microenvironment: Driven aromatic-ring cleavage microbes and aromatic compounds precursor biodegradation during sludge composting

The aim of this study was to clarify the aromatic cleavage pathways and microbes involved in the adverse effect of nitrate on aromatic compounds humic substances during sludge composting. Results showed that the functional microbes involved in aromatic compounds humic substances precursors (catechol, tyrosine, tryptophan and phenylalanine) cleavage pathways significantly enriched after nitrate addition. Linear regression analysis showed that aromatic-ring cleavage functional microbes exhibited significant negative correlation with aromatic humic substances (p < 0.05). Furthermore, network analysis indicated that most of microbial communities prefer cooperative with aromatic-ring cleavage functional microbes. Structural equation model further revealed that composting microenvironment drove aromatic-ring cleavage functional microbes activities, resulting in the biodegradation of complex aromatic compounds. This study parsed the effect of a negative factor on aromatic compounds humic substances from an opposing perspective. Properly controlling nitrate concentration and aromatic-ring cleavage functional microbes involved in precursors cleavage was suggested to the practice of composting.

Microbial Roles in Dissolved Organic Matter Transformation in Full-Scale Wastewater Treatment Processes Revealed by Reactomics and Comparative Genomics

Understanding the degradation of dissolved organic matter (DOM) is vital for optimizing DOM control. However, the microbe-mediated DOM transformation during wastewater treatment remains poorly characterized. Here, microbes and DOM along full-scale biotreatment processes were simultaneously characterized using comparative genomics and high-resolution mass spectrometry-based reactomics. Biotreatments significantly increased DOM's aromaticity and unsaturation due to the overproduced lignin and polyphenol analogs. DOM was diversified by over five times in richness, with thousands of nitrogenous and sulfur-containing compounds generated through microbe-mediated oxidoreduction, functional group transfer, and C-N and C-S bond formation. Network analysis demonstrated microbial division of labor in DOM transformation. However, their roles were determined by their functional traits rather than taxa. Specifically, network and module hubs exhibited rapid growth potentials and broad substrate affinities but were deficient in xenobiotics-metabolism-associated genes. They were mainly correlated to liable DOM consumption and its transformation to recalcitrant compounds. In contrast, connectors and peripherals were potential degraders of recalcitrant DOM but slow in growth. They showed specialized associations with fewer DOM molecules and probably fed on metabolites of hub microbes. Thus, developing technologies (e.g., carriers) to selectively enrich peripheral degraders and consequently decouple the liable and recalcitrant DOM transformation processes may advance DOM removal.