Tetracycline and quinolone contamination mediate microbial and antibiotic resistant gene composition in epiphytic biofilms of mesocosmic wetlands.

The fate and ecological impact of antibiotics on aquatic ecosystems have not been properly elucidated in mesocosm wetlands scale. This study explored how tetracyclines (TCs, including tetracycline TC and oxytetracycline) and fluoroquinolones (QNs, including ciprofloxacin CIP and levofloxacin) affect mesocosm wetlands vegetated by V. spiralis, focusing on their impact on epiphytic biofilm microbial communities and antibiotic resistance genes (ARGs). Results showed that submerged plants absorbed more antibiotics than sediment. Both TCs and QNs disrupted microbial communities in different ways and increased eukaryotic community diversity in a concentration-dependent manner (2-4 mg/L for CIP, 4-8 mg/L for TC). TCs mainly inhibited epiphytic bacteria, while CIP increased bacterial phyla abundance. TC reduced Cyanobacteriota, Acidobacteriota, and Patescibacteria but increased Bacillota, Bacteroidota, and Armatimonadota. In contrast, CIP reduced Bacteroidota, Cyanobacteriota, and Gemmatimonadota but increased Bacillota, Planctomycetota, and Acidobacteriota. Significant differences in ARG profiles were observed between QNs and TCs, with TCs having a more substantial effect on ARGs due to their stronger impact on bacterial communities. Both antibiotics raised ARG levels with higher concentrations, particularly for multidrug resistance, tetracyclines, trimethoprim, sulfonamides, aminoglycosides, and fosfomycin, emphasizing their role in antimicrobial resistance. The study suggests that antibiotics can either stimulate or inhibit ARGs depending on their effects on bacterial communities. This study provides key evidence on the ecological mechanisms underlying the impact of TCs and QNs on epiphytic microbes of mesocosm wetlands.

Chemical signaling in biofilm-mediated biofouling.

Biofouling is the undesirable accumulation of living organisms and their metabolites on submerged surfaces. Biofouling begins with adhesion of biomacromolecules and/or microorganisms and can lead to the subsequent formation of biofilms that are predominantly regulated by chemical signals, such as cyclic dinucleotides and quorum-sensing molecules. Biofilms typically release chemical cues that recruit or repel other invertebrate larvae and algal spores. As such, harnessing the biochemical mechanisms involved is a promising avenue for controlling biofouling. Here, we discuss how chemical signaling affects biofilm formation and dispersion in model species. We also examine how this translates to marine biofouling. Both inductive and inhibitory effects of chemical cues from biofilms on macrofouling are also discussed. Finally, we outline promising mitigation strategies by targeting chemical signaling to foster biofilm dispersion or inhibit biofouling.

A positive contribution to nitrogen removal by a novel NOB in a full-scale duck wastewater treatment system.

Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2 -) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.

A global metagenomics-based analysis of BPA degradation and its coupling with nitrogen, sulfur, and methane metabolism in landfill leachates.

Microbial metabolism in landfill leachate systems is critically important in driving the degradation reactions of organic pollutants, including the emerging pollutant bisphenol A (BPA). However, little research has addressed the microbial degradation of BPA in landfill leachate and its interactions with nitrogen (N), sulfur (S), and methane (CH4) metabolism on a global scale. To this end, in this study on a global scale, an extremely high concentration of BPA was detected throughout the global landfill leachates. Subsequent reconstructive analyses of metagenomic datasets from 113 sites worldwide revealed that the predominant BPA-degrading microflora included Proteobacteria, Firmicutes, and Bacteroidota. Further metabolic analyses revealed that all four biochemical pathways involved in the degradation of BPA were achieved through biochemical cooperation between different bacterial members of the community. In addition, BPA degraders have also been found to actively collaborate synergistically with non-BPA degraders in the N and S removal as well as CH4 catabolism in landfill leachates. Collectively, this study not only provides insights into the dominant microbial communities and specific types of BPA-degrading microbial members in the community of landfill leachates worldwide, but also reveals the synergistic interactions between BPA mineralization and N, S, and CH4 metabolism. These findings offer valuable and important insights for future comprehensive and in-depth investigations into BPA metabolism in different environments.

The fate of antibiotic resistance genes in wastewater containing microalgae treated by chlorination, ultra-violet, and Fenton reaction.

Antibiotic resistance genes (ARGs) and bacteria (ARBs) in the effluent of wastewater treatment plants (WWTPs) are of utmost importance for the dissemination of ARGs in natural aquatic environments. Therefore, there is an urgent need for effective technologies to eliminate WWTP ARGs/ARBs and mitigate the associated risks posed by the discharged ARG in aquatic environments. To test the effective technology for eliminating ARGs/ARBs, we compared the removal of ARGs and ARBs by three different tertiary treatments, namely ultra-violet (UV) disinfection, chlorination disinfection, and Fenton oxidation. Then, the treated wastewater was co-cultured with Chlorella vulgaris (representative of aquatic biota) to investigate the fate of discharged ARGs into the aquatic environment. The results demonstrated that chlorination (at a chlorine concentration of 15 mg/L) and Fenton (at pH 2.73, with 0.005 mol/L Fe2+ and 0.0025 mol/L H2O2) treatment showed higher efficacy in ARG removal (1.8 - 4.17 logs) than UV treatment (15 min) (1.29 - 3.87 logs). Moreover, chlorine at 15 mg/L and Fenton treatment effectively suppressed ARB regeneration while UV treatment for 15 min could not. Regardless of treatments tested in this study, the input of treated wastewater to the Chlorella system increased the number of ARGs and mobile genetic elements (MGEs), indicating the potential risk of ARG dissemination associated with WWTP discharge. Among the wastewater-Chlorella co-culture systems, chlorination resulted in less of an increase in the number of ARGs and MGEs compared to Fenton and UV treatment. When comparing the wastewater systems to the co-culture systems, it was observed that Chlorella vulgaris reduced the number of ARGs and MGEs in chlorination and UV-treated wastewater; however, Chlorella vulgaris promoted ARG survival in Fenton-treated water, suggesting that aquatic microalgae might act as a barrier to ARG dissemination. Overall, chlorination treatment not only effectively removes ARGs and inhibits ARB regeneration but also shows a lower risk of ARG dissemination. Therefore, chlorination is recommended for practical application in controlling the spread of discharged ARGs from WWTP effluent in natural aquatic environments.

Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China.

Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.

Dominance by cyanobacteria in the newly formed biofilms on stone monuments under a protective shade at the Beishiku Temple in China.

Following the installation of a protective shade, rapid propagation of microorganisms showing in black and grey colors occurred at Beishiku Temple in Gansu Province of China. This study employed a combination of high-throughput sequencing technology, morphological examinations, and an assessment of the surrounding environmental condition to analyze newly formed microbial disease spots. The investigation unveiled the responsible microorganisms and the instigating factors of the microbial outbreak that subsequently to the erection of the shade. Through comparison of bioinformatics, the ASV method surpasses the OTU method in characterizing community compositional changes by the dominant microbial groups, the phylum Cyanobacteria emerged as the most dominant ones in the microbial community accountable for the post-shade microbial deterioration. The black spot and grey spot are predominantly composed of Mastigocladopsis and Scytonema, respectively. Validation analysis, based on the active RNA-level community results, supported and validated these conclusions. Comparative scrutiny of the microbial community before shade installation and the background environmental data disclosed that the erection of the shade prompted a decrease in temperatures and an increase in humidity within the protected area. Consequently, this spurred the exponential proliferation of indigenous cyanobacteria in the spots observed. The outcomes of this study carry considerable significance in devising preventive conservation strategies for cultural heritage and in managing the process of biodeterioration.

Reforestation of Cunninghamia lanceolata changes the relative abundances of important prokaryotic families in soil.

Over the past decades, many forests have been converted to monoculture plantations, which might affect the soil microbial communities that are responsible for governing the soil biogeochemical processes. Understanding how reforestation efforts alter soil prokaryotic microbial communities will therefore inform forest management. In this study, the prokaryotic communities were comparatively investigated in a secondary Chinese fir forest (original) and a reforested Chinese fir plantation (reforested from a secondary Chinese fir forest) in Southern China. The results showed that reforestation changed the structure of the prokaryotic community: the relative abundances of important prokaryotic families in soil. This might be caused by the altered soil pH and organic matter content after reforestation. Soil profile layer depth was an important factor as the upper layers had a higher diversity of prokaryotes than the lower ones (p < 0.05). The composition of the prokaryotic community presented a seasonality characteristic. In addition, the results showed that the dominant phylum was Acidobacteria (58.86%) with Koribacteraceae (15.38%) as the dominant family in the secondary Chinese fir forest and the reforested plantation. Furthermore, soil organic matter, total N, hydrolyzable N, and NH4+-N were positively correlated with prokaryotic diversity (p < 0.05). Also, organic matter and NO3--N were positively correlated to prokaryotic abundance (p < 0.05). This study demonstrated that re-forest transformation altered soil properties, which lead to the changes in microbial composition. The changes in microbial community might in turn influence biogeochemical processes and the environmental variables. The study could contribute to forest management and policy-making.

Metagenomic insight into the pathogenic-related characteristics and resistome profiles within microbiome residing on the Angkor sandstone monuments in Cambodia.

To reveal the characteristics of indigenous microbiome including the pathogenic-related ones on Angkor monuments in Cambodia and the distribution pattern of resistome at different locations, several sites, namely Angkor Wat, Bayon of Angkor Thom, and Prasat Preah Vihear with different exposure levels to tourists were selected to conduct the metagenomic analysis in this study. The general characteristics of the microbiome on these monuments were revealed, and the association between the environmental geo-ecological feature and the indigenous microbiome was delineated. The most common microbial groups included 6 phyla, namely Acidobacteria, Actinobacteria, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia on the monuments, but Firmicutes and Chlamydiae were the most dominant phyla found in bats droppings. The taxonomic family of Chitinophagaceae could serve as a signature microbial group for Preah Vihear, the less visited site. More importantly, the pathogenic-related characteristics of the microbiome residing on Angkor monuments were uncovered. A set of specific antibiotic resistance genes (ARGs) with cross-niches dispersal capacity (between the environmental microbiome and the microbiome within warm blood fauna) was identified to be high by the source tracking analysis based on ARGs profile varies in this study. Among the 10 ARG-types detected in this study, 6 of them are confined to resistance mechanism of antibiotic efflux-pump. The findings of this study provide new a new direction on public health management and implication globally at archaeological sites for tourism.

Microbial phylogenetic divergence between surface-water and sedimentary ecosystems drove the resistome profiles.

Antibiotic pollution and the evolution of antibiotic resistance genes (ARGs) are increasingly viewed as major threats to both ecosystem security and human health, and have drawn attention. This study investigated the fate of antibiotics in aqueous and sedimentary substrates and the impact of ecosystem shifts between water and sedimentary phases on resistome profiles. The findings indicated notable variations in the concentration and distribution patterns of antibiotics across various environmental phases. Based on the partition coefficient (Kd), the total antibiotic concentration was significantly greater in the surface water (1405.45 ng/L; 49.5 %) compared to the suspended particulate matter (Kd = 0.64; 892.59 ng/g; 31.4 %) and sediment (Kd = 0.4; 542.64 ng/g; 19.1 %). However, the relative abundance of ARGs in surface water and sediment was disproportionate to the abundance of antibiotics concentration, and sediments were the predominant ARGs reservoirs. Phylogenetic divergence of the microbial communities between the surface water and the sedimentary ecosystems potentially played important roles in driving the ARGs profiles between the two distinctive ecosystems. ARGs of Clinical importance; including blaGES, MCR-7.1, ermB, tet(34), tet36, tetG-01, and sul2 were significantly increased in the surface water, while blaCTX-M-01, blaTEM, blaOXA10-01, blaVIM, tet(W/N/W), tetM02, and ermX were amplified in the sediments. cfxA was an endemic ARG in surface-water ecosystems while the endemic ARGs of the sedimentary ecosystems included aacC4, aadA9-02, blaCTX-M-04, blaIMP-01, blaIMP-02, bla-L1, penA, erm(36), ermC, ermT-01, msrA-01, pikR2, vgb-01, mexA, oprD, ttgB, and aac. These findings offer a valuable information for the identification of ARGs-specific high-risk reservoirs.

Environmental processes and health implications potentially mediated by dust-borne bacteria.

Understanding microbial migration and survival mechanisms in dust events (DEs) can elucidate genetic and metabolic exchange between environments and help predict the atmospheric pathways of ecological and health-related microbial stressors. Dust-borne microbial communities have been previously characterized, but the impact and interactions between potentially active bacteria within transported communities remain limited. Here, we analysed samples collected during DEs in Israel, using amplicon sequencing of the 16S rRNA genes and transcripts. Different air trajectories and wind speeds were associated not only with the genomic microbial community composition variations but also with specific 16S rRNA bacterial transcripts. Potentially active dust-borne bacteria exhibited positive interactions, including carbon and nitrogen cycling, biotransformation of heavy metals, degradation of organic compounds, biofilm formation, and the presence of pathogenic taxa. This study provides insights into the potential interactive relationships and survival strategies of microorganisms within the extreme dust environment.

The factors controlling antibiotic resistance genes in different treatment processes of mainstream full-scale wastewater treatment plants.

The alteration of antibiotic resistance genes (ARGs) in wastewater has been less studied in wastewater treatment plants (WWTPs), making it difficult to assess ARGs' spreading risk comprehensively. Therefore, this study investigated the distribution and reduction of ARGs in the main process (Anaerobic-Anoxic-Oxic with Membrane Bio-Reactor (A2/O + MBR), Oxidation Ditch with sedimentation (OD), and Cyclic Activated Sludge System (CASS) with sedimentation) and disinfection process (Ultra-violet and Chlorination) of full-scale WWTPs. The wastewater was sampled before and after the different main process and disinfection process; then, the diversity and abundance of ARGs and mobile genetic genes (MGEs, helping the horizontal transfer of ARGs) in wastewater of different treatment stages were determined by a real-time high-throughput quantitative PCR (HT-qPCR) system. It was found that similar influents would result in similar ARGs in wastewater samples, independent of the treatment processes used. The main process could effectively reduce the abundance of ARGs and MGEs by 1.80-2.12 and 1.46-2.18 logarithm units, respectively. The main factors affecting ARGs were mainly wastewater quality index, especially COD, and MGEs like transposase and insertion sequences which were significantly associated with 66 and 48 subtypes of ARGs, respectively. Moreover, disinfection was more effective than the main process in inactivating antibiotic resistance bacteria (ARB), and the removal rate of ARB by disinfection reached 43.53 %-100 %. However, there are still risks of ARB regeneration (up to 4.22 log units) in the effluent of WWTPs. In the future, nutrient removal and disinfection process improvement is necessary to benefit ARG and ARB removal.

Microscopic evidence of sandstone deterioration and damage by fungi isolated from the Angkor monuments in simulation experiments.

The Angkor monuments have been registered on the World Cultural Heritage List of UNESCO, while the buildings built mostly of sandstone are suffering from serious deterioration and damage. Microorganisms are one of the leading causes for the sandstone deterioration. Identification of the mechanisms underlying the biodeterioration is of significance because it reveals the biochemical reaction involved so that effective conservation and restoration of cultural properties can be achieved. In this study, the fungal colonization and biodeterioration of sandstone in simulation experiments were examined using confocal reflection microscopy (CRM) and scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS). Aspergillus sp. strain AW1 and Paecilomyces sp. strain BY8 isolated from the deteriorated sandstone of Angkor Wat and Bayon of Angkor Thom, respectively, were inoculated and incubated with the sandstone used for construction of Angkor Wat. With CRM, we could visualize that strain AW1 tightly attached to and broke in the sandstone with extension of the hyphae. Quantitative imaging analyses showed that the sandstone surface roughness increased and the cavities formed under the fungal hyphae deepened during the incubation of strains AW1 and BY8. These highlighted that the massive growth of fungi even under the culture conditions was associated with the cavity formation of the sandstone and its expansion. Furthermore, SEM-EDS indicated the flat and Si-rich materials, presumably quartz and feldspar, were found frequently at the intact sandstone surface. But the flatness was lost during the incubation, possibly due to the detachment of the Si-rich mineral particles by the fungal deterioration. Consequently, this study proposed a biodeterioration model of the sandstone in that the hyphae of fungi elongated on the surface of the sandstone to penetrate into the soft and porous sandstone matrix, damaging the matrix and gradually destabilize the hard and Si-rich minerals, such as quartz and feldspar, to the collapse and cavities.

Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China.

Metagenomics and metaproteomics analyses were used to determine the microbial diversity and taxon composition, as well as the biochemical potentials of the microbiome on the sandstone of Beishiku Temple located in Northwest China. Taxonomic annotation of the metagenomic dataset revealed the predominant taxa of the stone microbiome on this cave temple with characteristics of resistance to harsh environmental conditions. Meanwhile, there were also taxa in the microbiome that showed sensitivity to environmental factors. The taxa distribution and the metabolic functional distribution patterns by the metagenome and metaproteome, respectively, showed clear differences. The high abundance of energy metabolism represented in the metaproteome suggested that there were active geomicrobiological cycles of elements within the microbiome. The taxa responsible for reactions in the nitrogen cycle from both metagenome and metaproteome supported a metabolically active nitrogen cycle, and the high activity of Comammox bacteria indicated the strong metabolic activity of ammonia oxidation to nitrate in the outdoor site. The SOX-related taxa involved in the sulfur cycle showed higher activity outdoors than indoors, and on the outdoor ground than at the outdoor cliff, as detected through metaproteomic analysis. The development of petrochemical industry in the vicinity resulting in the deposition of sulfur/oxidized sulfur via atmosphere may stimulate the physiological activity of SOX. Our findings provide metagenomic and metaproteomic evidence for microbially driven geobiochemical cycles that result in the biodeterioration of stone monuments.

Bats, monkeys and plants in the time of Covid-19 pandemic at Angkor monuments.

Knowledge of biodeterioration and protection of cultural heritage depends on the scientific understanding of the substratum materials, the ambient environment, the fauna and flora including the microorganisms so an overall picture can be constructed to serve as a basis for protection and management. Over the past more than 20 years of survey and research, an accumulated dataset is available on the mechanisms on the (bio)deterioration of stone monuments in Cambodia, involving interactions among water cycling and salt dynamics with the presence of a rich surface microbiome, the biofilms. However, during the Covid-19 period (2020-2022), because of a drastic drop on tourist population, the number of bats and monkeys are on the rising, which have an impact on the on-going protection efforts. At the same time, large trees around and on the cultural heritage sites are being managed by trimming and removal to decrease the potential risk and negative impacts from them. The new management scheme needs scientific results for the long-term successful protection of these cultural heritage. A close examination of these issues is also meaningful and important to the research new initiatives and policy to be implemented not only in Cambodia but also elsewhere.

Ecological distribution and function of comammox Nitrospira in the environment.

Complete ammonia oxidizers (Comammox) are of great significance for studying nitrification and expanding the understanding of the nitrogen cycle. Moreover, Comammox bacteria are also crucial in natural and engineered environments due to their role in wastewater treatment and maintaining the flux of greenhouse gases to the atmosphere. However, only few studies are there regarding the Comammox bacteria and their role in ammonia and nitrite oxidation in the environment. This review mainly focuses on summarizing the genomes of Nitrospira in the NCBI database. Ecological distribution of Nitrospira was also reviewed and the influence of environmental parameters on genus Nitrospira in different environments has been summarized. Furthermore, the role of Nitrospira in carbon cycle, nitrogen cycle, and sulfur cycle were discussed, especially the comammox Nitrospira. In addition, the overviews of current research and development regarding comammox Nitrospira, were summarized along with the scope of future research. KEY POINTS: • Most of Comammox Nitrospira are widely distributed in both aquatic and terrestrial ecosystems, but it has been studied less frequently in the extreme environments. • Comammox Nitrospira can be involved in different nitrogen transformation process, but rarely involved in nitrogen fixation. • The stable isotope and transcriptome techniques are important methods to study the metabolic function of comammox Nitrospira.

Community structures and biodeterioration processes of epilithic biofilms imply the significance of micro-environments.

Epilithic biofilms colonising outdoor stone monuments can intensify the deterioration processes of the stone materials and pose great challenges to their protection. In this study, biodiversity and community structures of the epilithic biofilms colonising the surfaces of five outdoor stone dog sculptures were characterised by high-throughput sequencing. Although they are exposed to the same envrionment in a small yard, the analysis of their biofilm populations revealed high biodiversity and species richness as well as great differences in community compostions. Interestingly, populations responsible for pigment production (e.g., Pseudomonas, Deinococcus, Sphingomonas and Leptolyngbya) and for nitrogen (e.g., Pseudomonas, Bacillus, and Beijerinckia) and sulfur cycling (e.g., Acidiphilium) were the core common taxa in the epilithic biofilms, suggesting the potential biodeterioration processes. Furthermore, significant positive corrolections of metal elements rich in stone with biofilm communities showed that epilithic biofilms could take in minerals of stone. Importantly, geochemical properties of soluble ions (higher concentration of SO42- than NO3-) and slightly acidic micro-environments on the surfaces suggest corrosion of biogenic sulfuric acids as a main mechanism of biodeterioration of the sculptures. Interestingly, relative abundacne of Acidiphilium showed a positive correlation with acidic micro-environments and SO42- concentrations, implying they could be an indicator of sulfuric acid corrosion. Together, our findings support that micro-environments are inportant to community assembly of epilithic biofilms and the biodeterioration processes involved.

Delineation of the complex microbial nitrogen-transformation network in an anammox-driven full-scale wastewater treatment plant.

Microbial-driven nitrogen removal is a crucial step in modern full-scale wastewater treatment plants (WWTPs), and the complexity of nitrogen transformation is integral to the various wastewater treatment processes. A full understanding of the overall nitrogen cycling networks in WWTPs is therefore a prerequisite for the further enhancement and optimization of wastewater treatment processes. In this study, metagenomics and metatranscriptomics were used to elucidate the microbial nitrogen removal processes in an ammonium-enriched full-scale WWTP, which was configured as an anaerobic-anoxic-anaerobic-oxic system for efficient nitrogen removal (99.63%) on a duck breeding farm. A typical simultaneous nitrification-anammox-denitrification (SNAD) process was established in each tank of this WWTP. Ammonia was oxidized by ammonia-oxidizing bacteria (AOB), archaea (AOA), and nitrite-oxidizing bacteria (NOB), and the produced nitrite and nitrate were further reduced to dinitrogen gas (N2) by anammox and denitrifying bacteria. Visible red anammox biofilms were formed successfully on the sponge carriers submerged in the anoxic tank, and the nitrogen removal rate by anammox reaction was 4.85 times higher than that by denitrification based on 15N isotope labeling and analysis. This supports the significant accumulation of anammox bacteria on the carriers responsible for efficient nitrogen removal. Two distinct anammox bacteria, named "Ca. Brocadia sp. PF01" and "Ca. Jettenia sp. PF02", were identified from the biofilm in this investigation. By recovering their genomic features and their metabolic capabilities, our results indicate that the highly active core anammox process found in PF01, suggests extending its niche within the plant. With the possible contribution of the dissimilatory nitrate reduction to ammonium (DNRA) reaction, enriching PF02 within the biofilm may also be warranted. Collectively, this study highlights the effective design strategies of a full-scale WWTP with enrichment of anammox bacteria on the carrier materials for nitrogen removal and therefore the biochemical reaction mechanisms of the contributing members.

An overlooked influence of reactive oxygen species on ammonia-oxidizing microbial communities in redox-fluctuating aquifers.

Reactive oxygen species (ROS) are ubiquitous in O2-perturbed aquifers, but their role in shaping ammonia-oxidizing microbial communities is not clear. This study examined the dynamic responses of ammonia-oxidizing microorganisms (AOMs) in redox-fluctuating aquifers to ROS via field investigation and in-lab verification using transcriptomes/ metatranscriptome and RT-qPCR. Ammonia-oxidizing archaea (AOA) dominated recharge aquifers with lower ROS levels, whereas ammonia-oxidizing bacteria (AOB) and heterotrophic nitrifying aerobic bacteria (HNB) predominated in discharge areas with higher ROS levels. Similar succession in AOM enrichments was found in that the dominant AOMs changed from AOA Nitrosopumilus to AOB Nitrosomonas with increasing ROS. Ammonia oxidation and antioxidant capacity differed significantly among three AOM isolates exposed to ROS. ROS decreased the amoA gene expression of AOA strain Nitrososphaera viennensis PLX03, accompanied by inhibited ammonia oxidation capacity. By contrast, the catalase and superoxide dismutase activities of the AOB strain Nitrosomonas oligotropha PLL12 and HNB strain Pseudomonas aeruginosa PLL01 increased, and the antioxidant genes katG, sodA, ahpC, and ahpF were significantly upregulated. These results demonstrate that ROS exert an important influence on AOMs in redox-fluctuating aquifers. This study improves our understanding of the ecological niches of AOMs in surface/subsurface environments.

Diversity and Composition of Culturable Microorganisms and Their Biodeterioration Potentials in the Sandstone of Beishiku Temple, China.

Microbial colonization on stone monuments leads to subsequent biodeterioration; determining the microbe diversity, compositions, and metabolic capacities is essential for understanding biodeterioration mechanisms and undertaking heritage management. Here, samples of epilithic biofilm and naturally weathered and exfoliated sandstone particles from different locations at the Beishiku Temple were collected to investigate bacterial and fungal community diversity and structure using a culture-based method. The biodeterioration potential of isolated fungal strains was analyzed in terms of pigmentation, calcite dissolution, organic acids, biomineralization ability, and biocide susceptibility. The results showed that the diversities and communities of bacteria and fungi differed for the different sample types from different locations. The population of culturable microorganisms in biofilm samples was more abundant than that present in the samples exposed to natural weathering. The environmental temperature, relative humidity, and pH were closely related to the variation in and distribution of microbial communities. Fungal biodeterioration tests showed that isolated strains four and five were pigment producers and capable of dissolving carbonates, respectively. Their biomineralization through the precipitation of calcium oxalate and calcite carbonate could be potentially applied as a biotechnology for stone heritage consolidation and the mitigation of weathering for monuments. This study adds to our understanding of culturable microbial communities and the bioprotection potential of fungal biomineralization.