Unraveling the diversity of sedimentary sulfate-reducing prokaryotes (SRP) across Tibetan saline lakes using epicPCR

Exposure of polyethylene microplastics affects sulfur migration and transformation in anaerobic system

Polyethylene (PE) microplastic, which is detected in various environmental media worldwide, also inevitably enters wastewater treatment plants, which may have an impact on anaerobic processes in wastewater treatment. In this work, the effect of PE microplastics on anaerobic sulfur transformation was explored. Experimental results showed that PE microplastics addition at 0.1%- 0.5% w/w promoted H2S production by 14.8%-27.4%. PE microplastics enhanced the release of soluble organic sulfur and inorganic sulfate, and promoted the bioprocesses of organosulfur compounds hydrolysis and sulfate reduction. Mechanism analysis showed that PE microplastics increased the content of electroactive components (e.g., protein and humic acids) contained in extracellular polymeric substances (EPS). In particular, PE microplastics increased the proportion and the dipole moment of α-helix, an important component involved in electron transfer contained in extracelluar protein, which provided more electron transfer sites and promoted the α-helix mediated electron transfer. These enhanced the direct electron transfer ability of EPSs, which might explain why PE microplastics facilitated the bioprocesses of organosulfur compounds hydrolysis and sulfate reduction. Correspondingly, metagenomic analysis revealed that PE microplastics increased the relative abundance of S2- producers (e.g., Desulfobacula and Desulfonema) and the relative abundance of functional genes involved in anaerobic sulfur transformation (e.g., PepD and cysD), which were beneficial to H2S production in anaerobic system.

Nitrate and oxygen significantly changed the abundance rather than structure of sulphate-reducing and sulphur-oxidising bacteria in water retrieved from petroleum reservoirs

Sulphate-reducing bacteria (SRB) are the main culprits of microbiologically influenced corrosion in water-flooding petroleum reservoirs, but some sulphur-oxidising bacteria (SOB) are stimulated when nitrate and oxygen are injected, which control the growth of SRB. This study aimed to determine the distributions of SRB and SOB communities in injection-production systems and to analyse the responses of these bacteria to different treatments involving nitrate and oxygen. Desulfovibrio, Desulfobacca, Desulfobulbus, Sulfuricurvum and Dechloromonas were commonly detected via 16S rRNA gene sequencing. Still, no significant differences were observed for either the SRB or SOB communities between injection and production wells. Three groups of water samples collected from different sampling sites were incubated. Statistical analysis of functional gene (dsrB and soxB) clone libraries and quantitative polymerase chain reaction showed that the SOB community structures were more strongly affected by the nitrate and oxygen levels than SRB clustered according to the sampling site; moreover, both the SRB and SOB community abundances significantly changed. Additionally, the highest SRB inhibitory effect and the lowest dsrB/soxB ratio were obtained under high concentrations of nitrate and oxygen in the three groups, suggesting that the synergistic effect of nitrate and oxygen level was strong on the inhibition of SRB by potential SOB.

Temporal profiling of sediment microbial communities in the Three Gorges Reservoir Area discovered time-dissimilarity patterns and multiple stable states

Microbial communities play vital roles in cycling nutrients and maintaining water quality in aquatic ecosystems. To better understand the dynamics of microbial communities and to pave way to effective ecological remediation, it's essential to reveal the temporal patterns of the communities and to identify their states. However, research exploring the dynamic changes of microbial communities needs a large amount of time-series data, which could be an extravagant requirement for a single study. In this research, we overcame this challenge by conducting a meta-analysis of years of accumulations of 16S rRNA high-throughput sequencing data from the Three Gorges Reservoir Area (TGRA), an ecological and environmental hotspot. For better understanding the microbial communities time-dissimilarity dynamics, three microbial communities time-dissimilarity patterns were hypothesized, and the linear pattern in the TGRA was validated. In addition, to explore the stability of microbial communities in the TGRA, two alternative stable states were revealed, and their differences in community richness, alpha diversity indices, community composition, ecological network topological properties, and metabolic functions were demonstrated. In short, two states of microbial communities showed distinct richness and alpha diversity indices, and the communities in one state were more dominated by Halomonas and Nitrosopumilaceae genera, facilitating nitrogen cycling metabolic processes; whilst the main genera of the other state were Bathyarchaeia and Methanosaeta, which favored methane-related metabolism. Moreover, different studies and environmental differences between mainstream and tributaries were attributed as the potential inducing factors of the state division. Our study provides a comprehensive insight into the dynamics and stability of microbial communities in the TGRA, and a reference for future studies on microbial community dynamics.

Risk control of antibiotics, antibiotic resistance genes (ARGs) and antibiotic resistant bacteria (ARB) during sewage sludge treatment and disposal: A review

Sewage sludge is an important reservoir of antibiotics, antibiotic resistance genes (ARGs), and antibiotic resistant bacteria (ARB) in wastewater treatment plants (WWTPs), and the reclamation of sewage sludge potentially threats human health and environmental safety. Sludge treatment and disposal are expected to control these risks, and this review summarizes the fate and controlling efficiency of antibiotics, ARGs, and ARB in sludge involved in different processes, i.e., disintegration, anaerobic digestion, aerobic composting, drying, pyrolysis, constructed wetland, and land application. Additionally, the analysis and characterization methods of antibiotics, ARGs, and ARB in complicate sludge are reviewed, and the quantitative risk assessment approaches involved in land application are comprehensively discussed. This review benefits process optimization of sludge treatment and disposal, with regard to environmental risks control of antibiotics, ARGs, and ARB in sludge. Furthermore, current research limitations and gaps, e.g., the antibiotic resistance risk assessment in sludge-amended soil, are proposed to advance the future studies.

Uncovering the diverse hosts of tigecycline resistance gene tet(X4) in anaerobic digestion systems treating swine manure by epicPCR

The tet(X4) gene is a clinically important tigecycline resistance gene and has shown high persistence in livestock-related environments. However, the bacterial hosts of tet(X4) remain unknown due to the lack of appropriate approaches. Herein, a culture-independent and high-throughput epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction) method was developed, optimized, and demonstrated for the identification of bacterial hosts carrying tet(X4) from environmental samples. Considering the high sequence similarity between tet(X4) and other tet(X)-variant genes, specific primers and amplification conditions were screened and optimized to identify tet(X4) accurately and link tet(X4) with the 16S rRNA gene, which were further validated using artificially constructed bacterial communities. The epicPCR targeting tet(X4) was applied for the identification of bacterial hosts carrying this resistance gene in anaerobic digestion systems treating swine manure. A total of 19 genera were identified as tet(X4) hosts, which were distributed in the phyla Proteobacteria, Bacteroidota, Firmicutes, and Caldatribacteriota. Sixteen genera and two phyla that were identified have not been previously reported as tet(X4) bacterial hosts. The results indicated that a far more diverse range of bacteria was involved in harboring tet(X4) than previously realized. Compared with the tet(X4) hosts determined by correlation-based network analysis and metagenomic binning, epicPCR revealed a high diversity of tet(X4) hosts even at the phylum level. The epicPCR method developed in this study could be effectively employed to reveal the presence of tet(X4) bacterial hosts from a holistic viewpoint.

Uncovering Bacterial Hosts of Class 1 Integrons in an Urban Coastal Aquatic Environment with a Single-Cell Fusion-Polymerase Chain Reaction Technology

Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbor class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction (PCR)) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multigene loci of interest. We also identified the Rhizobacter genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts toward hotspots of class 1 integron-mediated dissemination of AMR.

Spatial pattern and co-occurrence network of microbial community in response to extreme environment of salt lakes on the Qinghai-Tibet Plateau

Microbial communities are important components of alpine lakes, especially in extreme environments such as salt lakes. However, few studies have examined the co-occurrence network of microbial communities and various environmental factors in the water of salt lakes on the Qinghai-Tibet Plateau. From May to June 2019, nine samples from seven salt lakes with water salinity ranges from 13 to 267‰ on the Qinghai-Tibet Plateau were collected. There were great differences between low-salinity samples and high-salinity samples in the inorganic salt ion concentration, pH, and biodiversity. In addition, the microbial community sturcture in low-salinity samples and high-salinity samples differed, suggesting that each sample has its own specific species. The co-occurrence network suggests that salinity was the most important forcing factor. We believe that salinity and inorganic salt ions can result in differences in microbial community in different salt lakes. This sequencing survey of multiple salt lakes with various salinities on the Qinghai-Tibet Plateau enhances our understanding of the response of microbial communities to environmental heterogeneity.

Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco

The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.

Organic fertilizer potentiates the transfer of typical antibiotic resistance gene among special bacterial species

The propagation of antibiotic resistance genes (ARGs) in environments has evoked many attentions, however, how to identify their host pathogenic bacteria in situ remains a great challenge. Here we explored the bacterial host distribution and dissemination of a typical ARG, sul1 gene, in agricultural soils through the simultaneous detection of sul1 and its host 16S rRNA gene by emulsion paired isolation and concatenation PCR (epicPCR). Compared to chemical fertilizer, organic fertilizer (chicken manure) led to a higher prevalence of sul1 gene in the soil, and dominant bacterial hosts of sul1 gene were classified into Proteobacteria and Bacteroidetes phyla. Additionally, significant higher diversity of antibiotic resistance bacteria (ARB), higher rate of horizontal gene transfer (HGT), higher rate of mobile genetic elements (MGE) and higher proportion of pathogens were all observed in the treatment of organic fertilizer. This study alerts potential health risks of manure applications in agricultural soils.

The natural product biosynthesis potential of the microbiomes of Earth – Bioprospecting for novel anti-microbial agents in the meta-omics era

As we stand on the brink of the post-antibiotic era, we are in dire need of novel antimicrobial compounds. Microorganisms produce a wealth of so-called secondary metabolites and have been our most prolific source of antibiotics so far. However, rediscovery of known antibiotics from well-studied cultured microorganisms, and the fact that the majority of microorganisms in the environment are out of reach by means of conventional cultivation techniques, have led to the exploration of the biosynthetic potential in natural microbial communities by novel approaches. In this mini review we discuss how sequence-based analyses have exposed an unprecedented wealth of potential for secondary metabolite production in soil, marine, and host-associated microbiomes, with a focus on the biosynthesis of non-ribosomal peptides and polyketides. Furthermore, we discuss how the complexity of natural microbiomes and the lack of standardized methodology has complicated comparisons across biomes. Yet, as even the most commonly sampled microbiomes hold promise of providing novel classes of natural products, we lastly discuss the development of approaches applied in the translation of the immense biosynthetic diversity of natural microbiomes to the procurement of novel antibiotics.

High-Throughput Single-Cell Technology Reveals the Contribution of Horizontal Gene Transfer to Typical Antibiotic Resistance Gene Dissemination in Wastewater Treatment Plants

The spread of antibiotic resistance genes (ARGs) has gained much attention worldwide, while the contribution of vertical gene transfer (VGT) and horizontal gene transfer (HGT) is still elusive. Here, we improved an emerging high-throughput single-cell-based technology, emulsion, paired isolation, and concatenation polymerase chain reaction (epicPCR), by lengthening the sequence of ARG in the fused ARG-16S rRNA fragments to cover the variance of both ARG and its hosts. The improved epicPCR was applied to track the hosts of a widely detected ARG, sul1 gene, in five urban wastewater treatment plants (UWTPs) during two seasons. The sul1 host bacteria were highly diverse and mostly classified as Proteobacteria and Bacteroidetes. Clear seasonal divergence of α-diversity and interaction networks were present in the host community. The consensus phylogenetic trees of the sul1 gene and their host demonstrated incorrespondence on the whole and regularity on abundant groups, suggesting the important role of both HGT and VGT, respectively. The relative importance of these two ways was further measured; HGT (54%) generally played an equal or even more important role as VGT (46%) in UWTPs. The application of the improved epicPCR technology provides a feasible approach to quantify the relative contributions of VGT and HGT in environmental dissemination of ARGs.

One cell at a time: droplet-based microbial cultivation, screening and sequencing

Microbes thrive and, in turn, influence the earth's environment, but most are poorly understood because of our limited capacity to reveal their natural diversity and function. Developing novel tools and effective strategies are critical to ease this dilemma and will help to understand their roles in ecology and human health. Recently, droplet microfluidics is emerging as a promising technology for microbial studies with value in microbial cultivating, screening, and sequencing. This review aims to provide an overview of droplet microfluidics techniques for microbial research. First, some critical points or steps in the microfluidic system are introduced, such as droplet stabilization, manipulation, and detection. We then highlight the recent progress of droplet-based methods for microbiological applications, from high-throughput single-cell cultivation, screening to the targeted or whole-genome sequencing of single cells.

Distinctive distributions of halophilic Archaea across hypersaline environments within the Qaidam Basin of China

Halophilic Archaea are widely distributed globally in hypersaline environments. However, little is known of how dominant halophilic archaeal genera are distributed across environments and how they may co-associate across ecosystems. Here, the archaeal community composition and diversity from hypersaline environments (> 300 g/L salinity; total of 33 samples) in the Qaidam Basin of China were investigated using high-throughput Illumina sequencing of 16S rRNA genes. The archaeal communities (total of 3,419 OTUs) were dominated by the class Halobacteria (31.7-99.6% relative abundances) within the phylum Euryarchaeota (90.8-99.9%). Five predominant taxa, including Halorubrum, Halobacterium, Halopenitus, Methanothrix, and Halomicrobium, were observed across most samples. However, several distinct genera were associated with individual samples and were inconsistently distributed across samples, which contrast with previous studies of hypersaline archaeal communities. Additionally, co-occurrence network analysis indicated that five network clusters were present and potentially reflective of interspecies interactions among the environments, including three clusters (clusters II, III, and IV) comprising halophilic archaeal taxa within the Halobacteriaceae and Haloferacaceae families. In addition, two other clusters (clusters I and V) were identified that comprised methanogens. Finally, salinity comprising ionic concentrations (in the order of Na⁺ > Ca²⁺ > Mg²⁺) and pH were most correlated with taxonomic distributions across sample sites.