Nano- and microplastics drive the dynamic equilibrium of amoeba-associated bacteria and antibiotic resistance genes.

As emerging pollutants, microplastics have become pervasive on a global scale, inflicting significant harm upon ecosystems. However, the impact of these microplastics on the symbiotic relationship between protists and bacteria remains poorly understood. In this study, we investigated the mechanisms through which nano- and microplastics of varying sizes and concentrations influence the amoeba-bacterial symbiotic system. The findings reveal that nano- and microplastics exert deleterious effects on the adaptability of the amoeba host, with the magnitude of these effects contingent upon particle size and concentration. Furthermore, nano- and microplastics disrupt the initial equilibrium in the symbiotic relationship between amoeba and bacteria, with nano-plastics demonstrating a reduced ability to colonize symbiotic bacteria within the amoeba host when compared to their microplastic counterparts. Moreover, nano- and microplastics enhance the relative abundance of antibiotic resistance genes and heavy metal resistance genes in the bacteria residing within the amoeba host, which undoubtedly increases the potential transmission risk of both human pathogens and resistance genes within the environment. In sum, the results presented herein provide a novel perspective and theoretical foundation for the study of interactions between microplastics and microbial symbiotic systems, along with the establishment of risk assessment systems for ecological environments and human health.

Copper stress shapes the dynamic behavior of amoebae and their associated bacteria.

Amoeba-bacteria interactions are prevalent in both natural ecosystems and engineered environments. Amoebae, as essential consumers, hold significant ecological importance within ecosystems. Besides, they can establish stable symbiotic associations with bacteria. Copper plays a critical role in amoeba predation by either killing or restricting the growth of ingested bacteria in phagosomes. However, certain symbiotic bacteria have evolved mechanisms to persist within the phagosomal vacuole, evading antimicrobial defenses. Despite these insights, the impact of copper on the symbiotic relationships between amoebae and bacteria remains poorly understood. In this study, we investigated the effects of copper stress on amoebae and their symbiotic relationships with bacteria. Our findings revealed that elevated copper concentration adversely affected amoeba growth and altered cellular fate. Symbiont type significantly influenced the responses of the symbiotic relationships to copper stress. Beneficial symbionts maintained stability under copper stress, but parasitic symbionts exhibited enhanced colonization of amoebae. Furthermore, copper stress favored the transition of symbiotic relationships between amoebae and beneficial symbionts toward the host's benefit. Conversely, the pathogenic effects of parasitic symbionts on hosts were exacerbated under copper stress. This study sheds light on the intricate response mechanisms of soil amoebae and amoeba-bacteria symbiotic systems to copper stress, providing new insights into symbiotic dynamics under abiotic factors. Additionally, the results underscore the potential risks of copper accumulation in the environment for pathogen transmission and biosafety.

Community coalescence under variable hydrochemical conditions of the Chesapeake Bay shaped bacterial diversity and functional traits.

Community coalescence related to bacterial mixing events regulates community characteristics and affects the health of estuary ecosystems. At present, bacterial coalescence and its driving factors are still unclear. The present study used a dataset from the Chesapeake Bay (2017) to address how bacterial community coalescence in response to variable hydrochemistry in estuarine ecosystems. We determined that variable hydrochemistry promoted the deterioration of water quality. Temperature, orthophosphate, dissolved oxygen, chlorophyll a, Secchi disk depth, and dissolved organic phosphorus were the key environmental factors driving community coalescence. Bacteria with high tolerance to environmental change were the primary taxa accumulated in community coalescence, and the significance of deterministic processes to communities was revealed. Community coalescence was significantly correlated with the pathways of metabolism and organismal systems, and promoted the co-occurrence of antibiotic resistance and virulence factor genes. Briefly, community coalescence under variable hydrochemical conditions shaped bacterial diversity and functional traits, to optimise strategies for energy acquisition and lay the foundation for alleviating environmental pressures. However, potential pathogenic bacteria in community coalescence may be harmful to human health and environmental safety. The present study provides a scientific reference for ecological management of estuaries.

Unraveling the important role of comammox Nitrospira to nitrification in the coastal aquaculture system.

Increasing nitrogen (N) input to coastal ecosystems poses a serious environmental threat. It is important to understand the responses and feedback of N removal microbial communities, particularly nitrifiers including the newly recognized complete ammonia-oxidizers (comammox), to improve aquaculture sustainability. In this study, we conducted a holistic evaluation of the functional communities responsible for nitrification by quantifying and sequencing the key functional genes of comammox Nitrospira-amoA, AOA-amoA, AOB-amoA and Nitrospira-nxrB in fish ponds with different fish feeding levels and evaluated the contribution of nitrifiers in the nitrification process through experiments of mixing pure cultures. We found that higher fish feeding dramatically increased N-related concentration, affecting the nitrifying communities. Compared to AOA and AOB, comammox Nitrospira and NOB were more sensitive to environmental changes. Unexpectedly, we detected an equivalent abundance of comammox Nitrospira and AOB and observed an increase in the proportion of clade A in comammox Nitrospira with the increase in fish feeding. Furthermore, a simplified network and shift of keystone species from NOB to comammox Nitrospira were observed in higher fish-feeding ponds. Random forest analysis suggested that the comammox Nitrospira community played a critical role in the nitrification of eutrophic aquaculture ponds (40-70 µM). Through the additional experiment of mixing nitrifying pure cultures, we found that comammox Nitrospira is the primary contributor to the nitrification process at 200 µM ammonium. These results advance our understanding of nitrifying communities and highlight the importance of comammox Nitrospira in driving nitrification in eutrophic aquaculture systems.

Contralateral approach using microscope and tubular retractor system for ipsilateral decompression of lumbar degenerative lateral recess stenosis associated with narrow spinal canal.

Objective: To summarize the clinical effect of a single-center retrospective analysis of the contralateral approach with a microscope and tubular retractor system for ipsilateral decompression in patients with lumbar lateral recess stenosis and a narrow spinal canal. Methods: A total of 25 patients who underwent ipsilateral decompression surgery via a contralateral approach with microscope and tubular retractor system, performed by one surgeon at a single center were retrospectively examined. The width of the lamina fenestration was compared with the preoperative distance from the root of the spinous process to the dorsal articular facet, the bilateral articular facet change in the suprapedicle notch section on CT scan, and with the changes in transverse and sagittal diameters of the canal area on MRI. Clinical efficacy was assessed using the Japanese Orthopedic Association (JOA), Visual Analog Scale (VAS), and Oswestry Disability Index (ODI) scores. Results: In total, 25 patients were treated and the mean intraoperative time was 82.04 ± 12.48 min. There was no nerve injury, cerebrospinal fluid leakage, and infection complications. The postoperative CT revealed that the width of the contralateral laminar fenestration was less than the distance from the root of the spinous process to the dorsal articular facet. The residual widths of the ipsilateral articular facet and contralateral articular facet were greater than 2/3 of the preoperative articular facet width. The transverse and sagittal diameter of canal were significantly increased. The mean follow-up period was 12-16 months, and no recurrence or reoperation incidence were found at the last follow-up. When compared to pre-surgery, the ODI, VAS, and JOA scores were significantly improved after surgery (p < 0.05). Conclusion: Based on our single-center retrospective observation of 25 cases and combined with previous literature, the contralateral approach with a microscope and tubular retractor system for ipsilateral decompression in patients with lumbar lateral recess stenosis and a narrow spinal canal can reduce damage to the articular processes, and probably more conducive to the postoperative stability of the lumbar spine. This was a single center retrospective analysis with a small sample size and lacked randomized controlled trials (RCTs). However, larger-scale, multicenter RTCs are required for additional validation.

Cooperation among nitrifying microorganisms promotes the irreversible biotransformation of sulfamonomethoxine.

Ammonia-oxidizing microorganisms, including AOA (ammonia-oxidizing archaea), AOB (ammonia-oxidizing bacteria), and Comammox (complete ammonia oxidization) Nitrospira, have been reported to possess the capability for the biotransformation of sulfonamide antibiotics. However, given that nitrifying microorganisms coexist and operate as communities in the nitrification process, it is surprising that there is a scarcity of studies investigating how their interactions would affect the biotransformation of sulfonamide antibiotics. This study aims to investigate the sulfamonomethoxine (SMM) removal efficiency and mechanisms among pure cultures of phylogenetically distinct nitrifiers and their combinations. Our findings revealed that AOA demonstrated the highest SMM removal efficiency and rate among the pure cultures, followed by Comammox Nitrospira, NOB, and AOB. However, the biotransformation of SMM by AOA N. gargensis is reversible, and the removal efficiency significantly decreased from 63.84 % at 167 h to 26.41 % at 807 h. On the contrary, the co-culture of AOA and NOB demonstrated enhanced and irreversible SMM removal efficiency compared to AOA alone. Furthermore, the presence of NOB altered the SMM biotransformation of AOA by metabolizing TP202 differently, possibly resulting from reduced nitrite accumulation. This study offers novel insights into the potential application of nitrifying communities for the removal of sulfonamide antibiotics (SAs) in engineered ecosystems.

Mangrove sediments are environmental hotspots for pathogenic protists.

Mangrove sediments are unique ecosystems providing habitats for diverse organisms, especially microbial communities. However, little is known about the diversity and environmental risk of a critical group of microorganisms, the protists. To address this gap, we employed metagenome sequencing technologies to provide the first comprehensive view of the protistan community in the mangrove sediment. Our results surprisingly showed that parasitic protists dominated the protistan community in mangrove sediments, with an average abundance of 59.67%, one of the highest in all ecosystems on Earth. We also found that the relative abundance of protists decreased significantly (R = -0.21, p = 0.045) with latitude but increased with depths (R = 0.7099, p < 0.001). The parasitic communities were positively influenced by microbial (bacteria, fungi, and archaea) communities, including horizontal-scale and vertical-scale. In addition, sulfate and salinity had the most significant influence on the protistan community. Our findings provide new insights into our understanding of protistan variation in mangrove sediments, including abundance, composition, and possible functions, and indicate that mangrove sediments are hotspots for environmental pathogens, posing a potential risk to human health.

Efficient inactivation of amoeba spores and their intraspore bacteria by solar/chlorine: Kinetics and mechanisms.

Amoebae are widespread in water and serve as environment vectors for pathogens, which may threaten public health. This study evaluated the inactivation of amoeba spores and their intraspore bacteria by solar/chlorine. Dictyostelium discoideum and Burkholderia agricolaris B1qs70 were selected as model amoebae and intraspore bacteria, respectively. Compared to solar irradiation and chlorine, solar/chlorine enhanced the inactivation of amoeba spores and intraspore bacteria, with 5.1 and 5.2-log reduction at 20 min, respectively. The enhancement was similar in real drinking water by solar/chlorine under natural sunlight. However, the spore inactivation decreased to 2.97-log by 20 min solar/chlorine under oxygen-free condition, indicating that ozone played a crucial role in the spore inactivation, as also confirmed by the scavenging test using tert­butanol to scavenge the ground-state atomic oxygen (O(3P)) as a ozone precursor. Moreover, solar/chlorine induced the shape destruction and structural collapse of amoeba spores by scanning electron microscopy. As for intraspore bacteria, their inactivation was likely ascribed to endogenous reactive oxygen species. As pH increased from 5.0 to 9.0, the inactivation of amoeba spores decreased, whereas that of intraspore bacteria was similar at pH 5.0 and 6.5 during solar/chlorine treatment. This study first reports the efficient inactivation of amoeba spores and their intraspore pathogenic bacteria by solar/chlorine in drinking water.

The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity.

Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.

Synthetic phylogenetically diverse communities promote denitrification and stability.

Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.

Synthetic Denitrifying Communities Reveal a Positive and Dynamic Biodiversity-Ecosystem Functioning Relationship during Experimental Evolution.

Biodiversity is vital for ecosystem functions and services, and many studies have reported positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships in plant and animal systems. However, if the BEF relationship exists and how it evolves remains elusive in microbial systems. Here, we selected 12 Shewanella denitrifiers to construct synthetic denitrifying communities (SDCs) with a richness gradient spanning 1 to 12 species, which were subjected to approximately 180 days (with 60 transfers) of experimental evolution with generational changes in community functions continuously tracked. A significant positive correlation was observed between community richness and functions, represented by productivity (biomass) and denitrification rate, however, such a positive correlation was transient, only significant in earlier days (0 to 60) during the evolution experiment (180 days). Also, we found that community functions generally increased throughout the evolution experiment. Furthermore, microbial community functions with lower richness exhibited greater increases than those with higher richness. Biodiversity effect analysis revealed positive BEF relationships largely attributable to complementary effects, which were more pronounced in communities with lower richness than those with higher richness. This study is one of the first studies that advances our understanding of BEF relationships and their evolutionary mechanisms in microbial systems, highlighting the crucial role of evolution in predicting the BEF relationship in microbial systems. IMPORTANCE Despite the consensus that biodiversity supports ecosystem functioning, not all experimental models of macro-organisms support this notion with positive, negative, or neutral biodiversity-ecosystem functioning (BEF) relationships reported. The fast-growing, metabolically versatile, and easy manipulation nature of microbial communities allows us to explore well the BEF relationship and further interrogate if the BEF relationship remains constant during long-term community evolution. Here, we constructed multiple synthetic denitrifying communities (SDCs) by randomly selecting species from a candidate pool of 12 Shewanella denitrifiers. These SDCs differ in species richness, spanning 1 to 12 species, and were monitored continuously for community functional shifts during approximately 180-day parallel cultivation. We demonstrated that the BEF relationship was dynamic with initially (day 0 to 60) greater productivity and denitrification among SDCs of higher richness. However, such pattern was reversed thereafter with greater productivity and denitrification increments in lower-richness SDCs, likely due to a greater accumulation of beneficial mutations during the experimental evolution.

Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes.

BACKGROUND: Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches. RESULTS: Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments. CONCLUSIONS: In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.

Protozoa as Hotspots for Potential Pathogens in the Drinking Water of a Subtropical Megacity: Diversity, Treatment, and Health Risk.

Drinking water systems host a wide range of microorganisms essential for biosafety. However, one major group of waterborne pathogens, protozoa, is relatively neglected compared to bacteria and other microorganisms. Until now, little is known about the growth and fate of protozoa and their associated bacteria in drinking water systems. In this study, we aim to investigate how drinking water treatment affects the growth and fate of protozoa and their associated bacteria in a subtropical megacity. The results showed that viable protozoa were prevalent in the city's tap water, and amoebae were the major component of tap water protozoa. In addition, protozoan-associated bacteria contained many potential pathogens and were primarily enriched in amoeba hosts. Furthermore, this study showed that current drinking water disinfection methods have little effect on protozoa and their associated bacteria. Besides, ultrafiltration membranes unexpectedly served as an ideal growth surface for amoebae in drinking water systems, and they could significantly promote the growth of amoeba-associated bacteria. In conclusion, this study shows that viable protozoa and their associated bacteria are prevalent in tap water, which may present an emerging health risk in drinking water biosafety.

Environmental stress promotes the persistence of facultative bacterial symbionts in amoebae.

Amoebae are one major group of protists that are widely found in natural and engineered environments. They are a significant threat to human health not only because many of them are pathogenic but also due to their unique role as an environmental shelter for pathogens. However, one unsolved issue in the amoeba-bacteria relationship is why so many bacteria live within amoeba hosts while they can also live independently in the environments. By using a facultative amoeba- Paraburkholderia bacteria system, this study shows that facultative bacteria have higher survival rates within amoebae under various environmental stressors. In addition, bacteria survive longer within the amoeba spore than in free living. This study demonstrates that environmental stress can promote the persistence of facultative bacterial symbionts in amoebae. Furthermore, environmental stress may potentially select and produce more amoeba-resisting bacteria, which may increase the biosafety risk related to amoebae and their intracellular bacteria.

The neonicotinoid insecticide imidacloprid has unexpected effects on the growth and development of soil amoebae.

Neonicotinoid pesticides are the most widely used insecticides worldwide and have become a global environmental issue. Previous studies have shown that imidacloprid, the most used neonicotinoid, can negatively affect a wide range of organisms, including non-target insects, fish, invertebrates, and mammals. Imidacloprid can also accumulate and persist in soils, posing threats to the terrestrial ecosystem. However, we know little about one ecologically important group of organisms, the single-celled soil protists. In this study, we used a soil amoeba, Dictyostelium discoideum, to test whether and how imidacloprid affects the growth and development of soil amoebae. We provide the first empirical evidence that environmental concentrations of imidacloprid negatively impact the fitness and development of soil amoebae. In addition, the adverse effects did not show a dose-response relationship with increased imidacloprid concentrations, where no significant difference was observed among the treatment groups. Further transcriptome analyses showed that imidacloprid affected amoeba's key DEGs related to phagocytosis, cell division, morphogenesis, and cytochrome P450. Moreover, soil amoebae show both conserved and novel transcriptional responses to imidacloprid. In conclusion, this study has expanded the non-target list of imidacloprid from animals and plants to single-celled protists, and we believe the impact of neonicotinoid pesticides on the microbiome is significantly underestimated and deserves more studies.

Biotransformation of sulfamonomethoxine in a granular sludge system: Pathways and mechanisms.

The biotransformation of sulfamonomethoxine (SMM) was studied in an aerobic granular sludge (AGS) system to understand the role of sorption by microbial cells and extracellular polymeric substances (EPS) and the role of functional microbe/enzyme biodegradation. Biodegradation played a more important role than adsorption, while microbial cells covered with tightly bound EPS (TB-EPS) showed higher adsorption capacity than microbial cells themselves or microbial cells covered with both loosely bound EPS (LB-EPS) and TB-EPS. The binding tests between EPS and SMM and the spectroscopic analyses (3D-EEM, UV-Vis, and FTIR) were performed to obtain more information about the adsorption process. The data showed that SMM could interact with EPS by combining with aromatic protein compounds, fulvic acid-like substances, protein amide II, and nucleic acids. Batch tests with various substances showed that SMM removal rates were in an order of NH2OH (60.43 ± 2.21 µg/g SS) > NH4Cl (52.96 ± 0.30 µg/g SS) > NaNO3 (31.88 ± 1.20 µg/g SS) > NaNO2 (21.80 ± 0.42 µg/g SS). Hydroxylamine and hydroxylamine oxidoreductase (HAO) favored SMM biotransformation and the hydroxylamine-mediated biotransformation of SMM was more effective than others. In addition, both ammonia monooxygenase (AMO) and CYP450 were able to co-metabolize SMM. Analysis of UPLC-QTOF-MS indicated the biotransformation mechanisms, revealing that acetylation of arylamine, glucuronidation of sulfonamide, deamination, SO2 extrusion, and δ cleavage were the five major transformation pathways. The detection of TP202 in the hydroxylamine-fed Group C indicated a new biotransformation pathway through HAO. This study contributes to a better understanding of the biotransformation of SMM.

Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes.

Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning. However, how such activities affect microbially driven methane (CH4), nitrogen (N), and sulfur (S) cycling of rhizosphere microbiomes remains unclear. To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres, we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies. Compared with the native mangrove (Kandelia obovata, KO), the introduced mangrove (Sonneratia apetala, SA) rhizosphere microbiome had significantly (p < 0.05) higher average genome size (AGS) (5.8 vs. 5.5 Mb), average 16S ribosomal RNA gene copy number (3.5 vs. 3.1), relative abundances of mobile genetic elements, and functional diversity in terms of the Shannon index (7.88 vs. 7.84) but lower functional potentials involved in CH4 cycling (e.g., mcrABCDG and pmoABC), N2 fixation (nifHDK), and inorganic S cycling (dsrAB, dsrC, dsrMKJOP, soxB, sqr, and fccAB). Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere. Additionally, salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes. This study advances our understanding of microbially mediated biogeochemical cycling of CH4, N, and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions, which has important implications for future mangrove reforestation.

Niche differentiation among comammox (Nitrospira inopinata) and other metabolically distinct nitrifiers.

Due to global change, increasing nutrient input to ecosystems dramatically affects the nitrogen cycle, especially the nitrification process. Nitrifiers including ammonia-oxidizing archaea (AOAs), ammonia-oxidizing bacteria (AOBs), nitrite-oxidizing bacteria (NOBs), and recently discovered complete ammonia oxidizers (comammoxs) perform nitrification individually or in a community. However, much remains to be learned about their niche differentiation, coexistence, and interactions among those metabolically distinct nitrifiers. Here, we used synthetic microbial ecology approaches to construct synthetic nitrifying communities (SNCs) with different combinations of Nitrospira inopinata as comammox, Nitrososphaera gargensis as AOA, Nitrosomonas communis as AOB, and Nitrospira moscoviensis as NOB. Our results showed that niche differentiation and potential interactions among those metabolically distinct nitrifiers were determined by their kinetic characteristics. The dominant species shifted from N. inopinata to N. communis in the N4 community (with all four types of nitrifiers) as ammonium concentrations increased, which could be well explained by the kinetic difference in ammonia affinity, specific growth rate, and substrate tolerance of nitrifiers in the SNCs. In addition, a conceptual model was developed to infer niche differentiation and possible interactions among the four types of nitrifiers. This study advances our understanding of niche differentiation and provides new strategies to further study their interactions among the four types of nitrifiers.

Host-Endosymbiont Relationship Impacts the Retention of Bacteria-Containing Amoeba Spores in Porous Media.

Amoebae are protists that are commonly found in water, soil, and other habitats around the world and have complex interactions with other microorganisms. In this work, we investigated how host-endosymbiont interactions between amoebae and bacteria impacted the retention behavior of amoeba spores in porous media. A model amoeba species, Dictyostelium discoideum, and a representative bacterium, Burkholderia agricolaris B1qs70, were used to prepare amoeba spores that carried bacteria. After interacting with B. agricolaris, the retention of D. discoideum spores was enhanced compared to noninfected spores. Diverse proteins, especially proteins contributing to the looser exosporium structure and cell adhesion functionality, are secreted in higher quantities on the exosporium surface of infected spores compared to that of noninfected ones. Comprehensive examinations using a quartz crystal microbalance with dissipation (QCM-D), a parallel plate chamber, and a single-cell force microscope present coherent evidence that changes in the exosporium of D. discoideum spores due to infection by B. agricolaris enhance the connections between spores in the suspension and the spores that were previously deposited on the collector surface, thus resulting in more retention compared to the uninfected ones in porous media. This work provides novel insight into the retention of amoeba spores after bacterial infection in porous media and suggests that the host-endosymbiont relationship regulates the fate of biocolloids in drinking water systems, groundwater, and other porous environments.

PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes.

BACKGROUND: Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database. RESULTS: In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments. CONCLUSIONS: We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.