Identification of bacterial communities in conventional wastewater treatment sludge to inform inoculation of the anammox process

This study uses 16 S rRNA gene pyrosequencing for the identification of a vast number of wastewater bacterial communities to investigate the evolution of bacterial communities in the Anammox process. Four lab-scale Anammox reactors inoculated with different conventional wastewater treatment sludge (activated sludge, livestock wastewater treatment sludge, denitrification sludge, and anaerobic digestion sludge) were operated under identical operating conditions for more than 400 days. The phylum Planctomycetes was present in all seeds of conventional sludge with a relative abundance of 1-3%. In particular, the known Anammox bacteria Candidatus Brocadia was found in the seed of the denitrification sludge. The reactor inoculated with denitrification sludge demonstrated the most effective nitrogen removal of ∼80% with successful cultivation of Anammox bacteria. This study found that the performance of the Anammox process is related to the presence of Nitrospira genus (nitrite-oxidizing bacteria) and that symbiotic association with other functional groups can lead to nitrogen removal. The outcomes of this study can provide vital insight into the study of microbial ecology for the cultivation of Anammox bacteria.

Seasonal variation of temperature affects HMW-PAH accumulation in fishery species by bacterially mediated LMW-PAH degradation

Currently, the specific mechanism generating seasonal variation in polycyclic aromatic hydrocarbons (PAHs) via bacterial biodegradation remains unclear, and whether this alteration affects PAH bioaccumulation is unknown. Therefore, we performed a study between 2015 and 2020 to investigate the effects of seasonal variation on bacterial communities and PAH bioaccumulation in the Pearl River Estuary. Significantly high PAH concentrations in both aquatic and fishery species were determined in dry seasons (the mean ∑₁₆PAH concentration: water, 37.24 ng/L (2015), 30.83 ng/L (2020); fish, 51.01 ng/L (2015) and 72.60 ng/L (2020)) compared to wet seasons (the mean ∑₁₆PAH concentration: water, 22.38 ng/L (2015), 19.40 ng/L(2020); fish, 25.28 ng/L (2015) and 32.59 ng/L (2020)). Distinct differences in taxonomic and functional composition of bacterial communities related to biodegradation of low molecular weight PAHs (LMW-PAHs) were observed between seasons, and the concentrations of PAHs were negatively correlated with seasonal variation in temperature. Temperature-related specific bacterial taxa (e.g., Stenotrophomonas) directly or indirectly participated in LMW-PAH degradation via encoding PAH degradation enzymes (e.g., protocatechuate 4,5-dioxygenase) that subsequently led to bioaccumulation of high molecular weight PAHs (HMW-PAHs) in wild and fishery species due to LMW-PAHs in the water. Based on this alteration, the ecological risk posed by PAHs decreased in wet seasons, and an unbalanced spatio-temporal distribution of PAHs was observed in this estuary. These results suggest that seasonal variation of temperature affects HMW-PAH accumulation in fishery species via bacterially mediated LMW-PAH biodegradation.

Changes in Bacterial Community Structure Across the Different Life Stages of Black Soldier Fly (Hermetia illucens)

The digestive capacity of organic compounds by the black soldier fly (BSF, Hermetia illucens, Diptera: Stratiomyidae, Linnaeus, 1758) is known to rely on complex larva-microbiota interactions. Although insect development is known to be a driver of changes of bacterial communities, the fluctuations along BSF life cycle in terms of composition and diversity of bacterial communities are still unknown. In this work, we used a metabarcoding approach to explore the differences in bacterial diversity along all four BSF developmental stages: eggs, larvae, pupae, and adult. We detected not only significant differences in bacterial community composition and species richness along the development of BSF, but also nine prevalent amplicon single variants (ASVs) forming the core microbiota. Out of the 2010 ASVs identified, 160 were significantly more abundant in one of the life stages. Moreover, using PICRUSt2, we inferred 27 potential metabolic pathways differentially used among the BSF life cycle. This distribution of metabolic pathways was congruent with the bacterial taxonomic distribution among life stages, demonstrating that the functional requirements of each phase of development are drivers of bacterial composition and diversity. This study provides a better understanding of the different metabolic processes occurring during BSF development and their links to changes in bacterial taxa. This information has important implications for improving bio-waste processing in such an economically important insect species.

Changes in bacterial community structures in soil caused by migration and aging of microplastics

Microplastics (MPs) are classified as emerging pollutants and greatly threatens soil ecosystems. To determine the impact of microplastic migration on soil bacterial diversity, we conducted a 90-day indoor soil column simulation test. Soil and microplastic (granular polystyrene, polypropylene MPs) samples were collected from different soil layers on days 30, 60, and 90. The downward migration trend of MPs was obvious, and its surface functional groups, hydrophobic properties, and crystallinity changed. Bacterial diversity was significantly higher in the surrounding soil than on microplastic surfaces. Also, the topsoil has more bacterial diversity than the middle soil. A higher number of OTUs were detected on microplastic surfaces for the middle soil than in the topsoil. Proteobacteria abundance on microplastic surfaces in the topsoil gradually increased over the course of the experiment, while an opposite trend was observed for the middle soil. Nevertheless, Proteobacteria abundances in both layers were higher than in the surrounding soils. MPs alters the bacterial community composition of soils and provides unique substrates for colonization. The impacts of MPs on soil bacterial communities were better understood in this study. Our findings highlighted the relevance of MPs in soil ecosystems as well as the potential threats they pose.

Effects of composting pig manure at different mature stages on ARGs in different types of soil-vegetable systems

Aerobic composting is considered as an economically as well as environmentally friendly technology that prevents the diffusion of ARGs and ARBs from manure to farmland soil, on which many studies have been conducted. However, the transmission route and potential ecological risks of ARGs in soil-vegetable systems after application of manure at different maturity stages remain unclear. Therefore, through a pot experiment, this study analyzed the effects of manure composted from livestock excrement on ARGs and microbial community in different soil-vegetable systems, taking leafy plants (Shanghai green) and tuber plants (carrot) as examples. It was noted that the highly matured manure could reduce the ARGs contamination in soil and crops, and the ARGs in soil tended to accumulate in the direction of plant roots. The edible part of crops often had a more serious ecological risk of ARGs, and the potential pathogenic bacteria and ARGs could harm human health through exposure and dietary routes. In summary, this study provides new evidence for the transmission of ARGs in soil-vegetable systems with different mature stages of manure and highlights the potential safety risks of the transfer of antibiotic resistance from manure to soil and ultimately to the human food chain.

Understanding point-of-use tap water quality: From instrument measurement to intelligent analysis using sample filtration

In most cases, point-of-use tap water quality is not routinely monitored due to widely-dispersed sampling sites and the costly tests. Although previous studies have revealed the variation of drinking water quality during distribution in municipal networks, the influence of aging pipes in buildings on quality is still unknown and this makes it difficult for water utilities to conduct regular maintenance. Herein, we have undertaken a survey of tap water samples across 8 districts in Beijing (China) to evaluate the potential effects of pipe age on point-of-use water quality, including turbidity, organic matter characteristics, and bacterial community. By grouping the collected samples according to the pipe age and source water respectively, the results suggested that bacterial diversity is significantly influenced by the pipe age. However, bacterial community structure is clearly influenced by the source water. Similarly, aging pipes in buildings are also responsible for the deterioration of the final water quality, and their effects have been closely linked to selected water quality parameters by evaluating the relevant factors. Moreover, the interrelationships between physico-chemical parameters and bacteria abundance were identified. For example, pH, Ca²⁺, Mg²⁺, Na⁺ and K⁺ showed a positive relationship with Bacillus abundance. In addition, an intelligent analysis method for understanding pipe age, organic matter concentration, and hardness (i.e., Ca²⁺ and Mg²⁺ concentration), based on image analysis of filtered membranes has been developed. The accuracy of prediction was encouraging, but can be improved with the collection of more data from tap water samples. We expect that this method can be exploited by the public to monitor their tap water and provide a feasible and cost-effective approach for water suppliers to locate aging/deteriorating pipes which need to be replaced or maintained.

Composition and distribution of bacterial communities and antibiotic resistance genes in fish of four mariculture systems

Fish-related antibiotic resistance genes (ARGs) have attracted attention for their potentially harmful effects on food safety and human health through the food chain transfer. However, the potential factors affecting these ARGs have not been fully explored. In this study, ARGs and bacterial communities in the fish gut, mucosal skin, and gill filaments in fish were comprehensively evaluated in four different mariculture systems formed by hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), Gracilaria bailinae, and Litopenaeus vannamei using different combinations. The results showed that 9 ARGs were detected in the gut and mucosal skin and 6 ARGs in the gill filaments. The detection rate of aphA1 was the highest, and the abundance was 1.91 × 10^-3 - 6.30 × 10^-2 copies per 16 S rRNA gene. Transposase gene (tnpA-04) was detected in all samples with the abundance of 3.57 × 10^-3 - 3.59 × 10^-2 copies per 16 S rRNA gene, and was strongly correlated with multiple ARGs (e.g., aphA1, tet(34), mphA-02). Proteobacteria, Deinococcus-Thermus, Firmicutes, and Bacteroidetes were the dominant phyla in the four mariculture systems, accounting for 65.1%-96.2% of the total bacterial community. Notably, the high relative abundance of Stenotrophomonas, a potential human pathogen, was elevated by 20.5% in the hybrid grouper gut in the monoculture system. In addition, variation partitioning analysis (VPA) showed that the difference in bacterial communities between mariculture systems was the main driving factor of ARGs distribution differences in hybrid groupers. This study provides a new comprehensive understanding of the characterization of fish-related ARGs contamination in different mariculture systems and facilitates the assessment of potential risks of ARGs and pathogen taxa to human health.

A Matter of Metals: Copper but Not Cadmium Affects the Microbial Alpha-Diversity of Soils and Sediments - a Meta-analysis

Heavy metal (HM) accumulation in soil affects plants and soil fauna, yet the effect on microbial alpha-diversity remains unclear, mainly due to the absence of dedicated research synthesis (e.g. meta-analysis). Here, we report the first meta-analysis of the response of soil microbial alpha-diversity to the experimental addition of cadmium (Cd) and copper (Cu). We considered studies conducted between 2013 and 2022 using DNA metabarcoding of bacterial and fungal communities to overcome limitations of other cultivation- and electrophoresis-based techniques. Fungi were discarded due to the limited study number (i.e. 6 studies). Bacterial studies resulted in 66 independent experiments reported in 32 primary papers from four continents. We found a negative dose-dependent response for Cu but not for Cd for bacterial alpha-diversity in the environments, only for Cu additions exceeding 29.6 mg kg^-1 (first loss of - 0.06% at 30 mg kg^-1). The maximal loss of bacterial alpha-diversity registered was 13.89% at 3837 mg kg^-1. Our results first highlight that bacterial communities behave differently to soil pollution depending on the metal. Secondly, our study suggests that even extreme doses of Cu do not cause a dramatic loss in alpha-diversity, highlighting how the behaviour of bacterial communities diverges from soil macro-organisms.

Metagenomic insights into the antibiotic resistome in freshwater and seawater from an Antarctic ice-free area

The comprehensive profiles of antibiotic resistance genes (ARGs) in the Antarctic water environments and their potential health risks are not well understood. The present study characterized the bacterial community compositions and ARG profiles of freshwater (11 samples) and seawater (28 samples) around the Fildes Region (an ice-free area in Antarctica) using a shotgun metagenomic sequencing approach for the first time. There were significant differences in the compositions of the bacterial community and ARG profiles between freshwater and seawater. In the 39 water samples, 114 ARG subtypes belonging to 15 ARG types were detectable. In freshwater, the dominant ARGs were related to multidrug and rifamycin resistance. In seawater, the dominant ARGs were related to peptide, multidrug, and beta-lactam resistance. Both the bacterial community compositions and ARG profiles were significantly related to certain physicochemical properties (e.g., pH, salinity, NO₃^-). Procrustes analysis revealed a significant correlation between the bacterial community compositions and ARG profiles of freshwater and seawater samples. A total of 31 metagenome-assembled genomes (MAGs) carrying 35 ARG subtypes were obtained and identified. The results will contribute to a better evaluation of the ARG contamination in relation to human health in the Antarctic aquatic environments.

Responses of microbial communities and metabolic profiles to the rhizosphere of Tamarix ramosissima in soils contaminated by multiple heavy metals

Heavy metals (HMs) contamination around smelters poses serious stress to soil microbiome. However, the co-effect of multiple HMs and native vegetation rhizosphere on the soil ecosystem remains unclear. Herein, effects of high HMs level and the rhizosphere (Tamarix ramosissima) on soil bacterial community structure and metabolic profiles in sierozem were analyzed by coupling high-throughput sequencing and soil metabolomics. Plant roots alleviated the threat of HMs by absorbing and stabilizing them in soil. High HMs level decreased the richness and diversity of soil bacterial community and increased numbers of special bacteria. Plant roots changed the contribution of HMs species shaping the bacterial community. Cd and Zn were the main contributors to bacterial distribution in non-rhizosphere soil, however, Pb and Cu became the most important HMs in rhizosphere soil. HMs induced more dominant metal-tolerant bacteria in non-rhizosphere than rhizosphere soil. Meanwhile, critical metabolites varied by rhizosphere in co-occurrence networks. Moreover, the same HMs-tolerant bacteria were regulated by different metabolites, e.g. unclassified family AKYG1722 was promoted by Dodecanoic acid in non-rhizosphere soil, while promoted by Octadecane, 2-methyl- in rhizosphere soil. The study illustrated that high HMs level and rhizosphere affected soil properties and metabolites, by which soil microbial community structure was reshaped.

Distinct bacterial communities and resistance genes enriched by triclocarban-contaminated polyethylene microplastics in antibiotics and heavy metals polluted sewage environment

Knowledge gaps still surround the question of what biofilms form on contaminated microplastics (MPs) in the antibiotics and (or) heavy metals polluted sewage. In this work, the clean polyethylene microplastics (PE MPs) and triclocarban (TCC)-contaminated PE MPs were cultured in the sewage containing only ampicillin (AMP), only copper (Cu) and both AMP and Cu for 28 days. The results showed that the TCC on PE MPs (with concentration of 2.48 mg/g PE MPs) did not impede the adhesion of the bacteria and the formation of biofilm. Moreover, many potential pathogenic bacteria (Aquabacterium and Pseudoxanthomonas) and potential resistant bacteria (Stenotrophomonas) were more likely to attach on TCC-contaminated PE MPs compared with clean PE MPs. In addition, biofilms of TCC-contaminated PE MPs had highest potential pathogenic functions. TCC-contaminated PE MPs also caused the increases of various resistance genes in both biofilm and sewage. The co-occurrence of TCC, AMP and Cu might exert a stronger selective pressure on bacterial communities and promote the co-selection of resistance genes. In addition, TCC-contaminated PE MPs resulted in higher abundance of five mobile genetic elements (MGEs) (intI1, intI3, tnpA-04, IS613 and trb-C) in sewage, which might further promote the transmission of resistance genes.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Improving production of lactic acid and volatile fatty acids from dairy cattle manure and corn straw silage: Effects of mixing ratios and temperature

Anaerobic co-fermentation (AcoF) of dairy cattle manure (DCM) and corn straw silage (CSS) for producing lactic acid (LA) and volatile fatty acids (VFAs) was investigated. Batch experiments were conducted at seven different DCM/CSS ratios and at mesophilic and thermophilic temperatures. Results indicated that the highest concentration of LA was 17.50 ± 0.70 g/L at DCM:CSS ratio of 1:3 and thermophilic temperature, while VFAs was 18.23 ± 2.45 g/L at mono-CSS fermentation and mesophilic temperature. High solubilization of thermophilic conditions contributed to LA accumulation in AcoF process. Presence of the CSS increased the relative abundance of Lactobacillus for LA production at thermophilic. Meanwhile, the abundance of Bifidobacterium was increased when CSS was added at mesophilic, which could conduce to VFAs production. This study provides a new route for enhancing the biotransformation of DCM and CSS into short-chain fatty acids, potentially bringing economic benefits to agricultural waste treatment.

Impact of the surrounding environment on antibiotic resistance genes carried by microplastics in mangroves

The pollution of antibiotic resistance genes (ARGs) carried by microplastics (MPs) is a growing concern. Mangroves are located at the intersection of land and sea and are seriously affected by MP pollution. However, few studies have systematic research evaluating the transmission risk of ARGs carried by MPs in mangroves. We conducted in situ experiments by burying five different MPs (polypropylene, high-density polyethylene, polystyrene, polyethylene glycol terephthalate, and polycaprolactone particles) in mangroves with different surrounding environments. A total of 10 genes in the MPs of mangroves were detected using quantitative real-time polymerase chain reactions, including eight ARGs and two mobile genetic elements (MGEs). The abundance of ARGs in Guanhai park mangroves in living areas (GH) was higher than that of Gaoqiao mangroves in protected areas (GQ) and Beiyue dike mangroves in aquaculture pond areas (BY). Pathogenic bacteria, such as Acinetobacter, Bacillus, and Vibrio were found on the MP surfaces of the mangroves. The number of ARGs carried by multiple drug-resistant bacteria in the GH mangroves was greater than that in the GQ and BY mangroves. Moreover, the ARGs carried by MPs in GH mangroves had the highest potential transmission risk by horizontal gene transfer. Sociometric and environmental factors were the main drivers shaping the distribution characteristics of ARGs and MGEs. Polypropylene and high-density polyethylene particles are preferred substrates for obtaining diffuse ARGs. This study investigated the drivers of ARGs in the MPs of mangroves and provided essential guidance on the use and handling of plastics.

Associating changes in the bacterial community of rumen and faeces and milk fatty acid profiles in dairy cows fed high-starch or starch and oil-supplemented diets

The experiment reported in this research paper aimed to evaluate the effects of high-starch or starch and oil-supplemented diets on rumen and faecal bacteria, and explore links between the structure of bacterial communities and milk fatty acid (FA) profiles. We used four Holstein dairy cows in a 4 × 4 Latin square design. Cows were fed a diet rich in cereals (high-starch diet with 23% starch content on dry matter (DM) basis), a diet supplemented with saturated FA from Ca salts of palm oil + 18% DM starch, a diet with high content of monounsaturated FA (from extruded rapeseeds) + 18% DM starch or a diet rich in polyunsaturated FA (from extruded sunflower seeds) + 17% DM starch. At the end of each experimental period, cows were sampled for rumen and faecal contents, which were used for DNA extraction and amplicon sequencing. Partial least squares (PLS) regression analysis highlighted diet-related changes in both rumen and faecal bacterial structures. Sparse PLS discriminant analysis was further employed to identify biologically relevant operational taxonomical units (OTUs) driving these differences. Our results show that Butyrivibrio discriminated the high-starch diet and linked positively with higher concentrations of milk odd- and branched-chain FA. YS2-related OTUs were key taxa distinguishing diets supplemented with Ca salts of palm oil or sunflower seeds and correlated positively with linoleic acid in milk. Similarly, diets modulated faecal bacterial composition. However, correlations between changes in faecal and rumen bacteria were poor. With this work, we demonstrated that high-starch or lipid-supplemented diets affect rumen and faecal bacterial community structure, and these changes could have a knock-on effect on milk FA profiles.

Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge

Background

Selection of optimal computational strategies for analyzing metagenomics data is a decisive step in determining the microbial composition of a sample, and this procedure is complex because of the numerous tools currently available. The aim of this research was to summarize the results of crowdsourced sbv IMPROVER Microbiomics Challenge designed to evaluate the performance of off-the-shelf metagenomics software as well as to investigate the robustness of these results by the extended post-challenge analysis. In total 21 off-the-shelf taxonomic metagenome profiling pipelines were benchmarked for their capacity to identify the microbiome composition at various taxon levels across 104 shotgun metagenomics datasets of bacterial genomes (representative of various microbiome samples) from public databases. Performance was determined by comparing predicted taxonomy profiles with the gold standard.

Results

Most taxonomic profilers performed homogeneously well at the phylum level but generated intermediate and heterogeneous scores at the genus and species levels, respectively. kmer-based pipelines using Kraken with and without Bracken or using CLARK-S performed best overall, but they exhibited lower precision than the two marker-gene-based methods MetaPhlAn and mOTU. Filtering out the 1% least abundance species—which were not reliably predicted—helped increase the performance of most profilers by increasing precision but at the cost of recall. However, the use of adaptive filtering thresholds determined from the sample’s Shannon index increased the performance of most kmer-based profilers while mitigating the tradeoff between precision and recall.

Conclusions

kmer-based metagenomic pipelines using Kraken/Bracken or CLARK-S performed most robustly across a large variety of microbiome datasets. Removing non-reliably predicted low-abundance species by using diversity-dependent adaptive filtering thresholds further enhanced the performance of these tools. This work demonstrates the applicability of computational pipelines for accurately determining taxonomic profiles in clinical and environmental contexts and exemplifies the power of crowdsourcing for unbiased evaluation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08803-2.

Bacterial species metabolic interaction network for deciphering the lignocellulolytic system in fungal cultivating termite gut microbiota

Fungus-cultivating termite Odontotermes badius developed a mutualistic association with Termitomyces fungi for the plant material decomposition and providing a food source for the host survival. The mutualistic relationship sifted the microbiome composition of the termite gut and Termitomyces fungal comb. Symbiotic bacterial communities in the O. badius gut and fungal comb have been studied extensively to identify abundant bacteria and their lignocellulose degradation capabilities. Despite several metagenomic studies, the species-wide metabolic interaction pattern of bacterial communities in termite gut and fungal comb remains unclear. The bacterial species metabolic interaction network (BSMIN) has been constructed with 230 bacteria identified from the O. badius gut and fungal comb microbiota. The network portrayed the metabolic map of the entire microbiota and highlighted several inter-species biochemical interactions like cross-feeding, metabolic interdependency, and competition. Further, the reconstruction and analysis of the bacterial influence network (BIN) quantified the positive and negative pairwise influences in the termite gut and fungal comb microbial communities. Several key macromolecule degraders and fermentative microbial entities have been identified by analyzing the BIN. The mechanistic interplay between these influential microbial groups and the crucial glycoside hydrolases (GH) enzymes produced by the macromolecule degraders execute the community-wide functionality of lignocellulose degradation and subsequent fermentation. The metabolic interaction pattern between the nine influential microbial species has been determined by considering them growing in a synthetic microbial community. Competition (30%), parasitism (47%), and mutualism (17%) were predicted to be the major mode of metabolic interaction in this synthetic microbial community. Further, the antagonistic metabolic effect was found to be very high in the metabolic-deprived condition, which may disrupt the community functionality. Thus, metabolic interactions of the crucial bacterial species and their GH enzyme cocktail identified from the O. badius gut and fungal comb microbiota may provide essential knowledge for developing a synthetic microcosm with efficient lignocellulolytic machinery.

Comprehensive insights into profiles and bacterial sources of intracellular and extracellular antibiotic resistance genes in groundwater

Antibiotic resistance genes (ARGs), especially last-resort ARGs (LARGs), are receiving extensive attention as emerging environmental contaminants in groundwater. However, their prevalent intracellular and extracellular patterns and bacterial sources in groundwater remain unclear. Herein, groundwater samples were collected in Tianjin, and characterized based on the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs), as well as the resident bacterial communities and extracellular DNA (eDNA)-releasing bacterial communities. The quantitative real-time PCR assays showed that eARGs presented fewer subtypes than iARGs and generally displayed lower detection frequencies than the corresponding iARGs. Similarly, LARGs exhibited lower detection frequencies than common ARGs, but the total abundance showed no significant differences between them. Genes vanA and bla_VIM were the observed dominant LARGs, and aadA was the observed common ARG independent of location inside or outside the bacteria. Furthermore, the top 10 phyla showed much difference between the main eDNA-releasing bacteria and the dominant resident bacteria. Proteobacteria was the predominant resident bacterial phyla while dominating the source of eDNA in groundwater. Despite representing a minor portion of the abundance in the resident bacteria, Actinobacteriota, Acidobacteriota, and Chloroflex surprisingly accounted for a large majority of eDNA release. Co-occurrence patterns among persistent ARGs, the resident bacteria, and eDNA-releasing bacteria revealed that the dominant common iARG aadA and intracellular LARGs bla_VIM and vanA had significant positive correlations with Methylobacterium_Methylorubrum and Shewanella. Meanwhile, the dominant extracellular LARG bla_VIM may be released by bacteria belonging to at least five genera, including Ellin6067, Bifidobacterium, Blautia, Veillonella, and Dechloromonas. Collectively, the findings of this study extend our understanding regarding the distribution of ARGs and their bacterial sources in groundwater, and indicate the serious pollution of LARGs in groundwater, which poses potential risks to public health.

In situ synthesis of Fe-N co-doped carbonaceous nanocomposites using biogas residue as an effective persulfate activator for remediation of aged petroleum contaminated soils

Persulfate (PS)-based chemical oxidation is an effective method for the remediation of petroleum-contaminated soils, but higher concentrations of PS (3-40%) may lead to soil acidification (pH decreased by 1.8-6.2 units) and affect the microbial communities. In this study, Fe/N co-doped carbonaceous nanocomposites (Fe-N @ CN) that can efficiently activate PS were developed from biogas residue for the remediation of petroleum-contaminated soil. The as-obtained Fe-N@CN displayed that the Fe-based nanoparticles were encapsulated in graphitic nanosheets, with Fe₃C and FeN_0.0760 as the main bonding modes. The removal efficiency of total petroleum hydrocarbons (TPHs) reached 73.14% in 3 days with a PS dose of 2% and catalyst dose of 0.4%, and increased by 15.8% on adding 30 mmol/kg of β-cyclodextrin. The free-radical quenching experiment and electron paramagnetic resonance revealed that SO₄·^-,·OH, O₂·^-, and ¹O₂ were involved in the removal of TPHs. Because of the low PS dosage, the remediation process had no significant effect on the soil pH. During the remediation process, soil catalase activity was enhanced and then recovered, whereas the soil bacterial community, reflected by the operational taxonomic unit values, decreased and then recovered. TPH-degrading bacteria were produced in the Fe-N@CN/PS/soil system after chemical oxidation, further contributing to soil remediation.

Distribution and transfer of antibiotic resistance genes in different soil-plant systems

The extensive application of farm manure that is contaminated with pharmaceutical antibiotics not only causes substantial soil pollution but additionally leads to the input of antibiotic resistance genes (ARGs) into the soil. These ARGs would proliferate and affect human health via the food chain. The effects of cultivated crops and wild plants on ARGs in rhizosphere soil are unclear. Therefore, we chose potted plants of cultivated crops (pakchoi, lettuce, corn) and wild plants (barnyard grass, crabgrass, dog tail), and set up test groups, i.e., treatment group, antibiotic-contaminated soil; control group, no antibiotic-contaminated soil; and a blank group without plants. The aim was to explore differences in the distribution and transfer of ARGs in the soil-plant system between cultivated crops and wild plants and at the same time to explore the influence of bacterial community evolution on ARGs in the rhizosphere soil of cultivated crops and wild plants. We concluded that under the pressure of antibiotic selection, ARGs can be transferred to the root endophytes of plants through the soil and further to the phyllosphere of plants, and cultivated crops such as pakchoi and wild plants barnyard grass have a strong ability to transport ARGs. Regardless of cultivated crops or wild plants, the abundance of ARGs in rhizosphere soil can be substantially reduced by 66.53 ~ 85.35%. Redundancy analysis and network analysis indicated that bacterial community succession is the main mechanism affecting changes of ARGs in rhizosphere soil. The reduction of Firmicutes due to the plant was the main factor responsible for the reduction of the abundance of ARGs in rhizosphere soil. The tetA, tetG, tetX, sul2, and qnrS genes are highly related to some potential pathogens, and the health risks they bring are a red flag that deserves attention.

Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants : Habitat and Host Species Drive the Structure of Bacterial Communities of Two Neotropical Trap-Jaw Odontomachus Ants

Ants have long been known for their associations with other taxa, including macroscopic fungi and symbiotic bacteria. Recently, many ant species have had the composition and function of their bacterial communities investigated. Due to its behavioral and ecological diversity, the subfamily Ponerinae deserves more attention regarding its associated microbiota. Here, we used the V4 region of the 16S rRNA gene to characterize the bacterial communities of Odontomachus chelifer (ground-nesting) and Odontomachus hastatus (arboreal), two ponerine trap-jaw species commonly found in the Brazilian savanna ("Cerrado") and Atlantic rainforest. We investigated habitat effects (O. chelifer in the Cerrado and the Atlantic rainforest) and species-specific effects (both species in the Atlantic rainforest) on the bacterial communities' structure (composition and abundance) in two different body parts: cuticle and gaster. Bacterial communities differed in all populations studied. Cuticular communities were more diverse, while gaster communities presented variants common to other ants, including Wolbachia and Candidatus Tokpelaia hoelldoblerii. Odontomachus chelifer populations presented different communities in both body parts, highlighting the influence of habitat type. In the Atlantic rainforest, the outcome depended on the body part targeted. Cuticular communities were similar between species, reinforcing the habitat effect on bacterial communities, which are mainly composed of environmentally acquired taxa. Gaster communities, however, differed between the two Odontomachus species, suggesting species-specific effects and selective filters. Unclassified Firmicutes and uncultured Rhizobiales variants are the main components accounting for the observed differences. Our study indicates that both host species and habitat act synergistically, but to different degrees, to shape the bacterial communities in these Odontomachus species.

Antibiotic resistance genes and bacterial community distribution patterns in pig farms

Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, many studies have been carried out to investigate the role of gut microbiota as a pool of antibiotic resistance genes (ARGs) in human and animals. Both the structure and function of the gut bacterial community and related ARGs in pig remain unknown. In this study, we characterized the gut microbiomes and resistomes of fecal samples collected from sixteen pig farms located in sixteen cities of Shandong Province by metagenomic sequencing. Alpha diversity indicated that fecal samples from Dezhou (DZ) and Jinan (J) showed higher alpha diversity, and the lowest was from pig farms of Rizhao (RZ). Other pig farms showed similar alpha diversity. Besides, we found that the composition of gut bacterial among these pig farms varied greatly. Helcococcus massiliensis was the dominant bacterial species in pig farms of RZ and Zibo (ZB), while Prevotella sp. P5-92 occupied a superior proportion in Binzhou (BZ) and Yantai (YT). The proportion of Lactobacillus johnsonii was similar among farms of Qingdao (QD), Linyi (LY), Taian (TA), Weifang (WF), Weihai (WH), and YT. In total, 1112 ARGs were obtained and classified into 69 groups from 48 fecal samples. ARG abundance was higher in farms of Dongying (DY) and WH than others, while the lowest farms in BZ and ZB. Interestingly, it is found that BZ pig farm was exclusive, so the tetQ gene showed a higher abundance. In contrast, the load of APH(3') - IIIa in fecal samples from DY, J-1, LC, WF, and WH was high. Meanwhile, the most relevant ARGs and the corresponding microbes were screened out. Our metagenomic sequencing data provides new insights into the abundance, diversity, and structure of bacterial community in pig farms. Meanwhile, we screened ARG-carrying bacteria and explored the correlation between ARGs and bacterial community, which provide a comprehensive view of the pig fecial ARGs and microbes in different farms of Shandong.

Saltwater intrusion affecting NO2- accumulation in demersal fishery species by bacterially mediated N-cycling

To investigate the underlying effects of saltwater intrusion (SWI) on bottom aquatic ecosystems, a set of environmental parameters and the bacterial community were determined and analyzed by sampling bottom water and surface sediments at the Modaomen waterway of the Pearl River Estuary. Biodiversity of fishery species and their relationship with the environment variables were analyzed together. NO₃^- and NO₂^- concentration down-regulation and NH₄⁺ concentration up-regulation in water and sediment were observed along the resulting salinity gradient, indicating that SWI affected N-cycling. Further investigation via 16 s sequencing revealed that taxonomic and functional composition of the bacterial community in the sediment displayed greater discretization than in water, implying that SWI exerted a greater impact on the sedimentary bacterial community. Metagenomic sequencing showed that the sedimentary bacterial community was associated with NO₃^-, NO₂^-, and NH₄⁺ transformation under SWI, and that this was driven by salinity and conductivity. Nitrogen metabolism and denitrification related genes were expressed at higher levels in high salinity than in low salinity, consistent with the increased enzymatic activities of NiR and NR. The NO₂^- concentration in the muscle of six selected fishery species was significantly decreased by 11.15-65.74% (P < 0.05) along the salinity gradient, indicating that SWI reduced NO₂^- accumulation. The results suggest that SWI alleviates NO₂^- accumulation in demersal fishery species via bacterial mediation of N-cycling.

Composting temperature directly affects the removal of antibiotic resistance genes and mobile genetic elements in livestock manure

The high antibiotic resistance gene (ARGs) contents in livestock manure pose a potential risk to environment and human health. The heap composting with an ambient temperature and thermophilic composting are two methods for converting livestock manure into fertilizer. This study investigated the variations in ARGs and mobile genetic elements (MGEs) and revealed potential mechanisms for ARGs removal using the two composting methods. The ARGs abundance were enriched by 44-fold in heap composting, among them, the macrolide-resistance genes increased significantly. On the contrary, the ARGs were removed by 92% in thermophilic composting, among them, tetracycline-resistance genes decreased by 97%. The bacterial hosts of ARGs were associated with the variations of ARGs and MGEs. The tetO was correlated with the most diverse bacteria in heap composting, and Bacteroidetes was the major host bacteria. While tetT was correlated with the most diverse bacteria in thermophilic composting, and Proteobacteria was the major host bacteria. Structural equation models showed that the enrichment of ARGs in heap composting was mainly correlated with bacterial communities, whereas, the removal of ARGs in thermophilic composting was directly affect by MGEs. Composting temperature directly affected the variations in ARGs. Higher and lower temperatures significantly decreased and increased, respectively, ARGs and MGEs abundance levels.

Effect of LDPE and biodegradable PBAT primary microplastics on bacterial community after four months of soil incubation

Biodegradable plastics would be gradually degraded by microbes after being used and discarded, forming biodegradable microplastics (BMPs). It is however not clear if it, like conventional microplastics, can affect the original soil ecological balance. In this study, the non-degradable LDPE (low density polyethylene) was used as the reference primary microplastic, and the BMP PBAT (polyadipate/butylene terephthalate) was used as the test object. The effects of the amount of PBAT on soil physical-chemical properties, bacterial community were investigated using high throughput sequencing. The results showed that when the highest amount of PBAT applied was up to 250 times higher than the normal application amount, resulted in a certain dose-effect, and a higher amount of PBAT would reduce the content of NO₃^--N and TP. The lower amount of PBAT relatively increased the diversity of soil bacterial communities, and the relative abundance of the unique Azotobacter increased with increasing PBAT amount. The abundance of bacterial community in soil with different PBAT amounts was significantly correlated with the soil's physical-chemical properties. In addition, Mesorhizobium, TM7a and Azotobacter were observed to be highly tolerant bacteria in PBAT containing soil which can be actively explored to study the biodegradation of BMPs PBAT.