Deepening the knowledge of universal stress proteins in Haloferax mediterranei

Haloarchaea, like many other microorganisms, have developed defense mechanisms such as universal stress proteins (USPs) to cope with environmental stresses affecting microbial growth. Despite the wide distribution of these proteins in Archaea, their biochemical characteristics still need to be discovered, and there needs to be more knowledge about them focusing on halophilic Archaea. Therefore, elucidating the role of USPs would provide valuable information to improve future biotechnological applications. Accordingly, transcriptional expression of the 37 annotated USPs in the Haloferax mediterranei genome has been examined under different stress conditions. From a global perspective, finding a clear tendency between particular USPs and specific stress conditions was not possible. Contrary, data analysis indicates that there is a recruitment mechanism of proteins with a similar sequence able to modulate the H. mediterranei growth, accelerating or slowing it, depending on their number. In fact, only three of these USPs were expressed in all the tested conditions, pointing to the cell needing a set of USPs to cope with stress conditions. After analysis of the RNA-Seq data, three differentially expressed USPs were selected and homologously overexpressed. According to the growth data, the overexpression of USPs induces a gain of tolerance in response to stress, as a rule. Therefore, this is the only work that studies all the USPs in an archaeon. It represents a significant first base to continue advancing, not only in this important family of stress proteins but also in the field of biotechnology and, at an industrial level, to improve applications such as designing microorganisms resistant to stress situations. KEY POINTS: • Expression of Haloferax mediterranei USPs has been analyzed in stress conditions. • RNA-seq analysis reveals that most of the USPs in H. mediterranei are downregulated. • Homologous overexpression of USPs results in more stress-tolerant strains.

Engineering hyperthermophilic pullulanase to efficiently utilize corn starch for production of maltooligosaccharides and glucose

Pullulanase is a starch-debranching enzyme that hydrolyzes side chain of starch, oligosaccharides and pullulan. Nevertheless, the limited activities of pullulanases constrain their practical application. Herein, the hyperthermophilic type II pullulanase from Pyrococcus yayanosii CH1 (PulPY2) was evolved by synergistically engineering the substrate-binding pocket and active-site lids. The resulting mutant PulPY2-M2 exhibited 5-fold improvement in catalytic efficiency (kcat/Km) compared to that of PulPY2. PulPY2-M2 was utilized to develop a one-pot reaction system for efficient production of maltooligosaccharides. The maltooligosaccharides conversion rate of PulPY2-M2 reached 96.1%, which was increased by 5.4% compared to that of PulPY2. Furthermore, when employed for glucose production, the glucose productivity of PulPY2-M2 was 25.4% and 43.5% higher than that of PulPY2 and the traditional method, respectively. These significant improvements in maltooligosaccharides and glucose production and the efficient utilization of corn starch demonstrated the potential of the engineered PulPY2-M2 in starch sugar industry.

Ecological degradation of a fragile semi-arid wetland and the implications in its microbial community: The case study of Las Tablas de Daimiel National Park (Spain)

Las Tablas de Daimiel National Park (TDNP, Iberian Peninsula) is a semi-arid wetland of international significance for waterfowl and serves as a migratory route for various bird species. However, TDNP presents strong anthropization and fluctuating water levels, making it a highly fragile ecosystem. Water physico-chemical parameters and microbial diversity of the three domains (Bacteria-Archaea- Eukarya) were analysed in Zone A and Zone B of the wetland (a total of eight stations) during spring and summer, aiming to determine how seasonal changes influence the water quality, trophic status and ultimately, the microbial community composition. Additionally, Photosynthetically Active Radiation (PAR) was used to determine the trophic status instead of transparency using Secchi disk, setting the threshold to 20-40 μmol/sm2 for benthic vegetation growth. In spring, both zones of the wetland were considered eutrophic, and physico-chemical parameters as well as microbial diversity were similar to other wetlands, with most abundant bacteria affiliated to Actinobacteriota, Cyanobacteria, Bacteroidota, Gammaproteobacteria and Verrumicrobiota. Methane-related taxa like Methanosarcinales and photosynthetic Chlorophyta were respectively the most representative archaeal and eukaryotic groups. In summer, phytoplankton bloom led by an unclassified Cyanobacteria and mainly alga Hydrodictyon was observed in Zone A, resulting in an increase of turbidity, pH, phosphorus, nitrogen, chlorophyll-a and phycocyanin indicating the change to hypertrophic state. Microbial community composition was geographical and seasonal shaped within the wetland as response to changes in trophic status. Archaeal diversity decreases and methane-related species increase due to sediment disturbance driven by fish activity, wind, and substantial water depth reduction. Zone B in summer suffers less seasonal changes, maintaining the eutrophic state and still detecting macrophyte growth in some stations. This study provides a new understanding of the interdomain microbial adaptation following the ecological evolution of the wetland, which is crucial to knowing these systems that are ecological niches with high environmental value.

Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs

This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.

Calcium-based polymers for suppression of soil acidification by improving acid-buffering capacity and inhibiting nitrification

Soil acidification is a major threat to agricultural sustainability in tropical and subtropical regions. Biodegradable and environmentally friendly materials, such as calcium lignosulfonate (CaLS), calcium poly(aspartic acid) (PASP-Ca), and calcium poly γ-glutamic acid (γ-PGA-Ca), are known to effectively ameliorate soil acidity. However, their effectiveness in inhibiting soil acidification has not been studied. This study aimed to evaluate the effect of CaLS, PASP-Ca, and γ-PGA-Ca on the resistance of soil toward acidification as directly and indirectly (i.e., via nitrification) caused by the application of HNO3 and urea, respectively. For comparison, Ca(OH)2 and lignin were used as the inorganic and organic controls, respectively. Among the materials, γ-PGA-Ca drove the substantial improvements in the pH buffering capacity (pHBC) of the soil and exhibited the greatest potential in inhibiting HNO3-induced soil acidification via protonation of carboxyl, complexing with Al3+, and cation exchange processes. Under acidification induced by urea, CaLS was the optimal one in inhibiting acidification and increasing exchangeable acidity during incubation. Furthermore, the sharp reduction in the population sizes of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) confirmed the inhibition of nitrification via CaLS application. Therefore, compared to improving soil pHBC, CaLS may play a more important role in suppressing indirect acidification. Overall, γ-PGA-Ca was superior to PASP-Ca and CaLS in enhancing the soil pHBC and the its resistance to acidification induced by HNO3 addition, whereas CaLS was the best at suppressing urea-driven soil acidification by inhibiting nitrification. In conclusion, these results provide a reference for inhibiting soil re-acidification in intensive agricultural systems.

Enhanced lactic acid production from household food waste under hyperthermophilic conditions: Mechanisms and regulation

An annual production of about 500 million tons of household food waste (HFW) has been documented, resulting in significant implications for human health and the environment in the absence of appropriate treatment. The anaerobic fermentation of HFW in an open system offers the potential to recover high value-added products, lactic acid (LA), thereby simultaneously addressing waste treatment and enhancing resource recovery efficiency. Most of LA fermentation studies have been conducted under mesophilic and thermophilic conditions, with limited research on the production of LA through anaerobic fermentation under hyperthermophilic conditions. This study aimed to produce LA through anaerobic fermentation from HFW under hyperthermophilic conditions (70 ± 1 °C), while varying pH values (5.0 ± 0.1, 7.0 ± 0.1, and 9.0 ± 0.1), and compare the results with LA production under mesophilic (35 ± 1 °C) and thermophilic (52 ± 1 °C) conditions. The findings of this study indicated that the combination of hyperthermophilic conditions and a neutral pH (pH7_70) yielded the highest concentration of LA, measuring at 17.75 ± 1.51 g/L. The mechanism underlying the high yield of LA at 70 °C was elucidated through the combined analysis of organics dissolution, enzymes activities, and 16S rRNA microbiome sequencing.

Higher stochasticity in comammox Nitrospira community assembly in upland soils than the adjacent paddy soils at a regional scale

Understanding the assembly mechanisms of microbial communities, particularly comammox Nitrospira, in agroecosystems is crucial for sustainable agriculture. However, the large-scale distribution and assembly processes of comammox Nitrospira in agricultural soils remain largely elusive. We investigated comammox Nitrospira abundance, community structure, and assembly processes in 16 paired upland peanuts and water-logged paddy soils in south China. Higher abundance, richness, and network complexity of comammox Nitrospira were observed in upland soils than in paddy soils, indicating a preference for upland soils over paddy soils among comammox Nitrospira taxa in agricultural environments. Clade A.2.1 and clade A.1 were the predominant comammox Nitrospira taxa in upland and paddy soils, respectively. Soil pH was the most crucial factor shaping comammox Nitrospira community structure. Stochastic processes were found to predominantly drive comammox Nitrospira community assembly in both upland and paddy soils, with deterministic processes playing a more important role in paddy soils than in upland soils. Overall, our findings demonstrate the higher stochasticity of comammox Nitrospira in upland soils than in the adjacent paddy soils, which may have implications for autotrophic nitrification in acidic agricultural soils.

Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.

Associations between the rumen microbiota and carcass merit and meat quality in beef cattle

The rumen microbiota is important for energy and nutrient acquisition in cattle, and therefore its composition may also affect carcass merit and meat quality attributes. In this study, we examined the associations between archaeal and bacterial taxa in the rumen microbiota of beef cattle and 12 different attributes, including hot carcass weight (HCW), dressing percentage, ribeye area (REA), intramuscular fat content, marbling score, fat thickness, yield grade, moisture content, purge loss, and shear force. There were significant correlations between the relative abundance of certain archaeal and bacterial genera and these attributes. Notably, Selenomonas spp. were positively correlated with live weight and HCW, while also being negatively correlated with purge loss. Members of the Christensenellaceae R-7, Moryella, and Prevotella genera exhibited positive and significant correlations with various attributes, such as dressing percentage and intramuscular fat content. Ruminococcaceae UCG-001 was negatively correlated with live weight, HCW, and dressing percentage, while Acidaminococcus and Succinivibrionaceae UCG-001 were negatively correlated with intramuscular fat content, moisture content, and marbling score. Overall, our findings suggest that specific changes in the rumen microbiota could be a valuable tool to improve beef carcass merit and meat quality attributes. Additional research is required to better understand the relationship between the rumen microbiota and these attributes, with the potential to develop microbiome-targeted strategies for enhancing beef production. KEY POINTS: • Certain rumen bacteria were associated with carcass merit and meat quality • Moryella was positively correlated with intramuscular fat in beef carcasses • Acidaminococcus spp. was negatively correlated with marbling and intramuscular fat.

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.

Anticancer drugs impact the performance and prokaryotic microbiome of an aerobic granular sludge system operated in a sequential batch reactor

Increased concerns exist about the presence of anticancer drugs in wastewater. However, knowledge of the impacts of anticancer drugs on the performance of the system and microbial communities during wastewater treatment processes is limited. We examined the effect of three anticancer drugs commonly detected in influents of wastewater treatment plants applied at three different concentration levels on the performance, efficiency of anticancer drug removal, and prokaryotic microbiome in an aerobic granular sludge system (AGS) operated in a sequential batch reactor (SBR). We showed that an AGS can efficiently remove anticancer drugs, with removal rates in the range of 53-100% depending on the type of drug and concentration level. Anticancer drugs significantly decreased the abundance of total bacterial and archaeal communities, an effect that was linked to reduced nitrogen removal efficiency. Anticancer drugs also reduced the diversity, altered the prokaryotic community composition, reduced network complexity, and induced a decrease of a wide range of predicted bacterial functions. Specific bacterial taxa responsive to the addition of anticancer drugs with known roles in nitrification and denitrification were identified. This study shows anticancer drugs should be monitored in the future as they can induce changes in the performance and microbiome of wastewater treatment technologies.

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments

BACKGROUND

Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species.

RESULTS

We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea.

CONCLUSIONS

The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. Video Abstract.

Structures, functions, and regulatory networks of universal stress proteins in clinically relevant pathogenic Bacteria

Universal stress proteins are a class of proteins widely present in bacteria, archaea, plants, and invertebrates, playing essential roles in bacterial adaptation to various environmental stresses. The functions of bacterial universal stress proteins are versatile, including resistance to oxidative stress, maintenance of cell wall integrity, DNA damage repair, regulation of cell division and growth, among others. When facing stresses such as temperature changes, pH shifts, fluctuations in oxygen concentration, and exposure to toxins, these proteins can bind to specific DNA sequences and rapidly adjust bacterial metabolic pathways and gene expression patterns to adapt to the new environment. In summary, bacterial universal stress proteins play a crucial role in bacterial adaptability and survival. A comprehensive understanding of bacterial stress response mechanisms and the development of new antibacterial strategies are of great significance. This review summarizes the research progress on the structure, function, and regulatory factors of universal stress proteins in clinically relevant bacteria, aiming to facilitate deeper investigations by clinicians and researchers into universal stress proteins.

The regulation effect of preventing soil nitrogen loss using microbial quorum sensing inhibitors

Preventing soil nitrogen (N) losses driven by microbial nitrification and denitrification contributes to improving global environmental concerns caused by NO3--N leaching and N2O emission. Quorum sensing (QS) signals regulate nitrification and denitrification of N-cycling bacteria in pure culture and water treatment systems, and mediate the composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in activated sludge. However, whether disrupting QS could prevent soil N losses remains unclear. This study explored the feasibility of applying quorum sensing inhibitors (QSIs) as an innovative strategy to reduce N losses from agricultural soils. The two QSIs, penicillic acid and 4-iodo-N-[(3S)-tetrahydro-2-oxo-3-furanyl]-benzeneacetamide (4-iodo PHL), were more effective in reducing N losses than traditional inhibitors, including N-(n-butyl) thiophosphoric triamide and 3,4-dimethylpyrazole phosphate. After 36 days of aerobic incubation, penicillic acid and 4-iodo PHL inhibited nitrification by 39% and 68%, respectively. The inhibitory effects are attributed to the fact that 4-iodo PHL decreased the abundance of archaeal and bacterial amoA genes, as well as the relative abundance of Candidatus Nitrocosmicus (AOA), Candidatus Nitrososphaera (AOA), and Nitrospira (nitrite-oxidizing bacteria/comammox), while penicillic acid reduced archaeal amoA abundance and the relative abundance of Nitrosospira (AOB) and the microbes listed above. Penicillic acid also strongly inhibited denitrification (33%) and N2O emissions (61%) at the peak of N2O production (day 4 of anaerobic incubation) via decreasing nitrate reductase gene (narG) abundance and increasing N2O reductase gene (nosZ) abundance, respectively. Furthermore, the environmental risks of QSIs to microbial community structure and network stability, CO2 emissions, and soil animals were acceptable. Overall, QSIs have application potential in agriculture to reduce soil N losses and the associated effect on climate change. This study established a new method to mitigate N losses from the perspective of QS, and can serve as important basis of decreasing the environmental risks of agricultural non-point source pollution.

Archaeal ether lipids improve internalization and transfection with mRNA lipid nanoparticles

Neutral and positively charged archaeal ether lipids (AEL) have been studied for their utilization as novel delivery systems for pDNA, showing efficient immune response with a strong memory effect while lacking noticeable toxicity. Recent technological advances placed mRNA lipid nanoparticles (LNPs) at the forefront of next-generation delivery systems; however, no study has examined AELs in mRNA delivery yet. In this study, we investigated either a crude lipid extract or the purified tetraether lipid caldarchaeol from Sulfolobus acidocaldarius as potential novel excipients for mRNA LNPs. Depending on their molar share in the respective LNP, particle uptake, and mRNA expression levels could be increased by up to 10-fold in in vitro transfection experiments using both primary cell sources (HSMM) and established cell lines (Caco-2, C2C12) compared to a well-known reference formulation. This increased efficiency might be linked to a substantial effect on endosomal escape, indicating fusogenic and lyotropic features of AELs. This study shows the high value of archaeal ether lipids for mRNA delivery and provides a solid foundation for future in vivo experiments and further research.

Urea amendment decouples nitrification in hydrocarbon contaminated Antarctic soil

Hydrocarbon contaminated soils resulting from human activities pose a risk to the natural environment, including in the Arctic and Antarctic. Engineered biopiles constructed at Casey Station, Antarctica, have proven to be an effective strategy for remediating hydrocarbon contaminated soils, with active ex-situ remediation resulting in significant reductions in hydrocarbons, even in the extreme Antarctic climate. However, the use of urea-based fertilisers, whilst providing a nitrogen source for bioremediation, has also altered the natural soil chemistry leading to increases in pH, ammonium and nitrite. Monitoring of the urea amended biopiles identified rising levels of nitrite to be of particular interest, which misaligns with the long term goal of reducing contaminant levels and returning soil communities to a 'healthy' state. Here, we combine amplicon sequencing, microfluidic qPCR on field samples and laboratory soil microcosms to assess the impact of persistent nitrite accumulation (up to 60 months) on nitrifier abundances observed within the Antarctic biopiles. Differential inhibition of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) Nitrobacter and Nitrospira in the cold, urea treated, alkaline soils (pH 8.1) was associated with extensive nitrite accumulation (76 ± 57 mg N/kg at 60 months). When the ratio of Nitrospira:AOB dropped below ∼1:1, Nitrobacter was completely inhibited or absent from the biopiles, and nitrite accumulated. Laboratory soil microcosms (incubated at 7 °C and 15 °C for 9 weeks) reproduced the pattern of nitrite accumulation in urea fertilized soil at the lower temperature, consistent with our longer-term observations from the Antarctic biopiles, and with other temperature-controlled microcosm studies. Diammonium phosphate amended soil did not exhibit nitrite accumulation, and could be a suitable alternative biostimulant to avoid excessive nitrite build-up.

Enhancement of methane production from anaerobic digestion of Erigeron canadensis via O2-nanobubble water supplementation

Malignant invasive Erigeron canadensis, as a typical lignocellulosic biomass, is a formidable challenge for sustainable and efficient resource utilization, however nanobubble water (NBW) coupled with anaerobic digestion furnishes a prospective strategy with superior environmental and economic effectiveness. In this study, influence mechanism of various O2-NBW addition times on methanogenic performance of E. canadensis during anaerobic digestion were performed to achieve the optimal pollution-free energy conversion. Results showed that supplementation of O2-NBW in digestion system could significantly enhance the methane production by 10.70-16.17%, while the maximum cumulative methane production reached 343.18 mL g-1 VS in the case of one-time O2-NBW addition on day 0. Furthermore, addition of O2-NBW was conducive to an increase of 2-90% in the activities of dehydrogenase, α-glucosidase and coenzyme F420. Simultaneously, both facultative bacteria and methanogenic archaea were enriched as well, further indicating that O2-NBW might be responsible for facilitating hydrolytic acidification and methanogenesis. Based on Kyoto Encyclopedia of Genes and Genomes (KEGG) cluster analysis, provision of O2-NBW enhanced the metabolism of carbohydrate and amino acid, translation as well as membrane transport of bacteria and archaea. This study might offer the theoretical guidance and novel insights for efficient recovery of energy from lignocellulosic biomass on account of O2-NBW adhibition in anaerobic digestion system, progressing tenor of carbon-neutral vision.

Iron-mediated DAMO-anammox process: Revealing the mechanism of electron transfer

The nitrate denitrifying anaerobic methane oxidation-anaerobic ammonia oxidation (DAMO-anammox) can accomplish nitrogen removal and methane (CH4) reduction. This process greatly contributes to carbon emission mitigation and carbon neutrality. In this study, we investigated the electron transfer process of functional microorganisms in the iron-mediated DAMO-anammox system. Fe3+ could be bound to several functional groups (-CH3, COO-, -CH) in extracellular polymeric substance (EPS), and the functional groups bound were different at different iron concentration. Fe3+ underwent reduction reactions to produce Fe2+. Most Fe3+ and Fe2+ react with microorganisms and formed chelates with EPS. Three-dimensional fluorescence spectra showed that Fe3+ affected the secretion of tyrosine and tryptophan, which were essential for cytochrome synthesis. The presence of Fe3+ accelerated c-type cytochrome-mediated extracellular electron transfer (EET), and when more Fe3+ existed, the more cytochrome C expressed. DAMO archaea (M. nitroreducens) in the system exhibited a high positive correlation with the functional genes (resa and ccda) for cytochrome c synthesis. Some denitrifying microorganisms showed positive correlations with the abundance of riboflavin. This finding showed that riboflavin secreted by functional microorganisms acted as an electron shuttle. In addition, DAMO archaea were positively correlated with the hair synthesis gene pily1, which indicated that direct interspecies electron transfer (DIET) may exist in the iron-mediated DAMO-anammox system.

Competition between ammonia-oxidizing archaea and complete ammonia oxidizers from freshwater environments

Aerobic ammonia oxidizers (AOs) are prokaryotic microorganisms that contribute to the global nitrogen cycle by performing the first step of nitrification, the oxidation of ammonium to nitrite and nitrate. While aerobic AOs are found ubiquitously, their distribution is controlled by key environmental conditions such as substrate (ammonium) availability. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are generally found in oligotrophic environments with low ammonium availability. However, whether AOA and comammox share these habitats or outcompete each other is not well understood. We assessed the competition for ammonium between an AOA and comammox enriched from the freshwater Lake Burr Oak. The AOA enrichment culture (AOA-BO1) contained Nitrosarchaeum sp. BO1 as the ammonia oxidizer and Nitrospira sp. BO1 as the nitrite oxidizer. The comammox enrichment BO4 (cmx-BO4) contained the comammox strain Nitrospira sp. BO4. The competition experiments were performed either in continuous cultivation with ammonium as a growth-limiting substrate or in batch cultivation with initial ammonium concentrations of 50 and 500 µM. Regardless of the ammonium concentration, Nitrospira sp. BO4 outcompeted Nitrosarchaeum sp. BO1 under all tested conditions. The dominance of Nitrospira sp. BO4 could be explained by the ability of comammox to generate more energy through the complete oxidation of ammonia to nitrate and their more efficient carbon fixation pathway-the reductive tricarboxylic acid cycle. Our results are supported by the higher abundance of comammox compared to AOA in the sediment of Lake Burr Oak.

IMPORTANCE

Nitrification is a key process in the global nitrogen cycle. Aerobic ammonia oxidizers play a central role in the nitrogen cycle by performing the first step of nitrification. Ammonia-oxidizing archaea (AOA) and complete ammonia oxidizers (comammox) are the dominant nitrifiers in environments with low ammonium availability. While AOA have been studied for almost 20 years, comammox were only discovered 8 years ago. Until now, there has been a gap in our understanding of whether AOA and comammox can co-exist or if one strain would be dominant under ammonium-limiting conditions. Here, we present the first study characterizing the competition between freshwater AOA and comammox under varying substrate concentrations. Our results will help in elucidating the niches of two key nitrifiers in freshwater lakes.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

Understanding vermicompost and organic manure interactions: impact on toxic elements, nitrification activity, comammox Nitrospira inopinata, and archaea/bacteria

Vermicompost is a substantial source of nutrients, promotes soil fertility, and maintains or increases soil organic matter levels. Potentially toxic elements (PTEs) in vermicompost impact on nitrification activity. However, it is yet unknown how vermicompost affects nitrifying bacteria and archaea, comammox Nitrospira inopinata (complete ammonia oxidizers), net nitrification rates (NNRs), and PTEs. The effects of vermicompost application on NNRs, potential nitrification rates (NPs), PTEs, and the abundances of comammox N. inopinata bacteria, nitrite-oxidizing bacteria (NOB), and ammonia-oxidizing bacteria (AOB)/archaea (AOA) were studied. NNRs and NPs were significantly higher (p < 0.05) in fresh cow-dung vermicompost (stored for 40 days) as compared with other organic manure. The level of PTEs (Cu2+, Fe2+, Pb2+, Cd2+, and Zn2+) was significantly lower (p < 0.05) in vermicompost as compared with compost of waste material with Trichoderma and cow dung. Comammox N. inopinata, NOB, AOB, and AOA were significantly higher (p < 0.05) in stored cow-dung vermicompost (more than 1 year) as compared with other organic manure. The results of the scatterplot matrix analysis suggested that Fe2+, total nitrogen (TN), soil organic carbon (SOC), and total carbon (TC) were linearly correlated (p < 0.001) with NNRs and NPs in vermicompost and organic manure. Similarly, comammox N. inopinata bacteria, NOB, AOB, and AOA were linearly correlated (p < 0.001) with NNR and NP. These results indicated that vermicompost promoted nitrification activity by increasing microbial diversity and abundance, supplying nutrients and organic matter for microbial growth, and facilitating complex microbial interactions. It may be concluded that the influence of vermicompost, which played a great role in PTE concentration reduction, increased chemical, and biological properties, increased the growth rate of nitrifying bacteria/archaea and the nitrogen cycle.

Black yeasts in hypersaline conditions

Extremotolerant and extremophilic fungi are an important part of microbial communities that thrive in extreme environments. Among them, the black yeasts are particularly adaptable. They use their melanized cell walls and versatile morphology, as well as a complex set of molecular adaptations, to survive in conditions that are lethal to most other species. In contrast to extremophilic bacteria and archaea, these fungi are typically extremotolerant rather than extremophilic and exhibit an unusually wide ecological amplitude. Some extremely halotolerant black yeasts can grow in near-saturated NaCl solutions, but can also grow on normal mycological media. They adapt to the low water activity caused by high salt concentrations by sensing their environment, balancing osmotic pressure by accumulating compatible solutes, removing toxic salt ions from the cell using membrane transporters, altering membrane composition and remodelling the highly melanized cell wall. As protection against extreme conditions, halotolerant black yeasts also develop different morphologies, from yeast-like to meristematic. Genomic studies of black yeasts have revealed a variety of reproductive strategies, from clonality to intense recombination and the formation of stable hybrids. Although a comprehensive understanding of the ecological role and molecular adaptations of halotolerant black yeasts remains elusive and the application of many experimental methods is challenging due to their slow growth and recalcitrant cell walls, much progress has been made in deciphering their halotolerance. Advances in molecular tools and genomics are once again accelerating the research of black yeasts, promising further insights into their survival strategies and the molecular basis of their adaptations. KEY POINTS: • Black yeasts show remarkable adaptability to environmental stress • Black yeasts are part of microbial communities in hypersaline environments • Halotolerant black yeasts utilise various molecular and morphological adaptations.

Side effects of the addition of an adsorbent for the nitrification performance of a microbiome in the treatment of an antibiotic mixture

This work determined the effect of biochar (BC) as an adsorbent on the nitrifying microbiome in regulating the removal, transformation, fate, toxicity, and potential environmental consequences of an antibiotic mixture containing oxytetracycline (OTC) and sulfamethoxazole (SMX). Despite the beneficial role of BC as reported in the literature, the present study revealed side effects for the nitrifying microbiome and its functioning arising from the presence of BC. Long-term monitoring revealed severe disruption to nitratation via the inhibition of both nitrite oxidizers (e.g., Nitrospira defluvii) and potential comammox species (e.g., Ca. Nitrospira nitrificans). Byproducts (BPs) more toxic than the parent compounds were found to persist at a high relative abundance, particularly in the presence of BC. Quantitative structure-activity relationship modeling determined that the physicochemical properties of the toxic BPs significantly differed from those of OTC and SMX. The results suggested that the BPs tended to mobilize and accumulate on the surface of the solids in the system (i.e., the BC and biofilm), disrupting the nitrifiers growing at the interface. Collectively, this study provides novel insights, demonstrating that the addition of adsorbents to biological systems may not necessarily be beneficial; rather, they may generate side effects for specific bacteria that have important ecosystem functions.

Methane emissions and the microbial community in flooded paddies affected by the application of Fe-stabilized natural organic matter

Redox chemistry involving the quinone/phenol cycling of natural organic matter (NOM) is known to modulate microbial respiration. Complexation with metals or minerals can also affect NOM solubilization and stability. Inspired by these natural phenomena, a new soil amendment approach was suggested to effectively decrease methane emissions in flooded rice paddies. Structurally stable forms of NOM such as lignin and humic acids (HAs) were shown to decrease methane gas emissions in a vial experiment using different soil types and rice straw as a methanogenic substrate, and this inhibitory behavior was likely enhanced by ferric ion-NOM complexation. A mechanistic study using HAs revealed that complexation facilitated the slow release of the humic components. Interestingly, borohydride-based reduction, which transformed quinone moieties into phenols, caused the HAs to lose their inhibitory capacity, suggesting that the electron-accepting ability of HAs is vital for their inhibitory effect. In rice field tests, the humic-metal complexes were shown to successfully mitigate methane generation, while carbon dioxide emissions were relatively unchanged. Microbial community analysis of the rice fields by season revealed a decrease in specific cellulose-metabolizing and methanogenic genera associated with methane emissions. In contrast, the relative abundance of Thaumarchaeota and Actinomycetota, which are associated with NOM and recalcitrant organics, was higher in the presence of Fe-stabilized HAs. These microbial dynamics suggest that the slow release of humic components is effective in modulating the anoxic soil microbiome, possibly due to their electron-accepting ability. Given the simplicity, cost-effectiveness, and soil-friendly nature of complexation processes, Fe-stabilized NOM represents a promising approach for the mitigation of methane emissions from flooded rice paddies.

Occurrence, characteristics, and microbial community of microplastics in anaerobic sludge of wastewater treatment plants

Wastewater treatment plants (WWTPs) usually contain microplastics (MPs) due to daily influents of domestic and municipal wastewater. Thus, the WWTPs act as a point source of MPs distribution in the environment due to their incapability to remove MPs completely. In this study, MPs occurrence and distribution in anaerobic sludge from WWTPs in different regions (Kaifeng "KHP", Jinan "JSP", and Lanzhou "LGP") were studied. Followed by MPs identification by microscopy and Fourier transform infrared (FTIR) spectrum. The microbial communities associated with anaerobic sludge and MPs were also explored. The results showed that MPs concentrations were 16.5, 38.5, and 17.2 particles/g of total solids (TS) and transparent MPs accounted for 49.1%, 58.5%, and 48.3% in KHP, JSP, and LGP samples, respectively. Fibers represented the most common shape of MPs in KHP (49.1%), JSP (56.0%), and LGP (69.0%). The FTIR spectroscopy indicated the predominance of polyethylene polymer in 1-5 mm MPs. The Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Planctomycetes were the abundant phyla in all anaerobic sludge. The bacterial genera in KHP and LGP were similar, in which Caldilinea (>23%), Terrimonas (>10%), and Ferruginibacter (>7%) formed the core bacterial genera. While Rhodococcus (15.3%) and Rhodoplanes (10.9%) were dominating in JSP. The archaeal genera Methanosaeta (>69%) and Methanobrevibacter (>10%) were abundant in KHP and LGP sludge. While Methanomethylovorans accounted for 90% of JSP. Acetyltransferase and hydratase were the major bacterial enzymes, while reductase was the key archaeal enzyme in all anaerobic sludge. This study provided the baseline for MPs distribution, characterization, and MPs associated microbes in WWTPs.

AOB Nitrosospira cluster 3a.2 (D11) dominates N2O emissions in fertilised agricultural soils

Ammonia-oxidation process directly contribute to soil nitrous oxide (N2O) emissions in agricultural soils. However, taxonomy of the key nitrifiers (within ammonia oxidising bacteria (AOB), archaea (AOA) and complete ammonia oxidisers (comammox Nitrospira)) responsible for substantial N2O emissions in agricultural soils is unknown, as is their regulation by soil biotic and abiotic factors. In this study, cumulative N2O emissions, nitrification rates, abundance and community structure of nitrifiers were investigated in 16 agricultural soils from major crop production regions of China using microcosm experiments with amended nitrogen (N) supplemented or not with a nitrification inhibitor (nitrapyrin). Key nitrifier groups involved in N2O emissions were identified by comparative analyses of the different treatments, combining sequencing and random forest analyses. Soil cumulative N2O emissions significantly increased with soil pH in all agricultural soils. However, they decreased with soil organic carbon (SOC) in alkaline soils. Nitrapyrin significantly inhibited soil cumulative N2O emissions and AOB growth, with a significant inhibition of the AOB Nitrosospira cluster 3a.2 (D11) abundance. One Nitrosospira multiformis-like OTU phylotype (OTU34), which was classified within the AOB Nitrosospira cluster 3a.2 (D11), had the greatest importance on cumulative N2O emissions and its growth significantly depended on soil pH and SOC contents, with higher growth at high pH and low SOC conditions. Collectively, our results demonstrate that alkaline soils with low SOC contents have high N2O emissions, which were mainly driven by AOB Nitrosospira cluster 3a.2 (D11). Nitrapyrin can efficiently reduce nitrification-related N2O emissions by inhibiting the activity of AOB Nitrosospira cluster 3a.2 (D11). This study advances our understanding of key nitrifiers responsible for high N2O emissions in agricultural soils and their controlling factors, and provides vital knowledge for N2O emission mitigation in agricultural ecosystems.

Effects of coal-fired power plants on soil microbial diversity and community structures

Long-term deposition of atmospheric pollutants emitted from coal combustion and their effects on the eco-environment have been extensively studied around coal-fired power plants. However, the effects of coal-fired power plants on soil microbial communities have received little attention through atmospheric pollutant deposition and coal-stacking. Here, we collected the samples of power plant soils (PS), coal-stacking soils (CSS) and agricultural soils (AS) around three coal-fired power plants and background control soils (BG) in Huainan, a typical mineral resource-based city in East China, and investigated the microbial diversity and community structures through a high-throughput sequencing technique. Coal-stacking significantly increased (p < 0.05) the contents of total carbon, total nitrogen, total sulfur and Mo in the soils, whereas the deposition of atmospheric pollutants enhanced the levels of V, Cu, Zn and Pb. Proteobacteria, Actinobacteria, Thaumarchaeota, Thermoplasmata, Ascomycota and Basidiomycota were the dominant taxa in all soils. The bacterial community showed significant differences (p < 0.05) among PS, CSS, AS and BG, whereas archaeal and fungal communities showed significant differences (p < 0.01) according to soil samples around three coal-fired power plants. The predominant environmental variables affecting soil bacterial, archaeal and fungal communities were Mo-TN-TS, Cu-V-Mo, and organic matter (OM)-Mo, respectively. Certain soil microbial genera were closely related to multiple key factors associated with stacking coal and heavy metal deposition from power plants. This study provided useful insight into better understanding of the relationships between soil microbial communities and long-term disturbances from coal-fired power plants.

Competitive enrichment of comammox Nitrospira in floccular sludge

The discovery of complete ammonium oxidation (comammox) has subverted the traditional perception of two-step nitrification, which plays a key role in achieving biological nitrogen removal from wastewater. Floccular sludge-based treatment technologies are being applied at the majority of wastewater treatment plants in service where detection of various abundances and activities of comammox bacteria have been reported. However, limited efforts have been made to enrich and subsequently characterize comammox bacteria in floccular sludge. To this end, a lab-scale sequencing batch reactor (SBR) in the step-feeding mode was applied in this work to enrich comammox bacteria through controlling appropriate operational conditions (dissolved oxygen of 0.5 ± 0.1 g-O2/m3, influent ammonium of 40 g-N/m3 and uncontrolled longer sludge retention time). After 215-d operation, comammox bacteria gradually gained competitive advantages over counterparts in the SBR with a stable nitrification efficiency of 92.2 ± 2.2 %: the relative abundance of Nitrospira reached 42.9 ± 1.3 %, which was 13 times higher than that of Nitrosomonas, and the amoA gene level of comammox bacteria increased to 7.7 ± 2.1 × 106 copies/g-biomass, nearly 50 times higher than that of conventional ammonium-oxidizing bacteria. The enrichment of comammox bacteria, especially Clade A Candidatus Nitrospira nitrosa, in the floccular sludge led to (i) apparent affinity constants for ammonium and oxygen of 3.296 ± 0.989 g-N/m3 and 0.110 ± 0.004 g-O2/m3, respectively, and (ii) significantly low N2O and NO production, with emission factors being 0.136 ± 0.026 % and 0.023 ± 0.013 %, respectively.

Acceleration of the biodegradation of cationic polyacrylamide by the coupling effect of thermophilic microorganisms and high temperature in hyperthermophilic composting

As a flocculant of sewage sludge, cationic polyacrylamide (CPAM) enters the environment with sludge and exists for a long time, posing serious threats to the environment. Due to the environmental friendliness and high efficiency in the process of organic solid waste treatment, hyperthermophilic composting (HTC) has received increasing attention. However, it is still unclear whether the HTC process can effectively remove CPAM from sludge. In this study, the effects of HTC and conventional thermophilic composting (CTC) on CPAM in sludge were compared and analyzed. At the end of HTC and CTC, the concentrations of CPAM were 278.96 mg kg-1 and 533.89 mg kg-1, respectively, and the removal rates were 72.17% and 46.61%, respectively. The coupling effect of thermophilic microorganisms and high temperature improved the efficiency of HTC and accelerated the biodegradation of CPAM. The diversity and composition of microbial community changed dramatically during HTC. Geobacillus, Thermobispora, Pseudomonas, Brevundimonas, and Bacillus were the dominant bacteria responsible for the high HTC efficiency. To our knowledge, this is the first study in which CPAM-containing sludge is treated using HTC. The ideal performance and the presence of key microorganisms revealed that HTC is feasible for the treatment of CPAM-containing sludge.

Analysis of the differences in physicochemical properties, volatile compounds, and microbial community structure of pit mud in different time spaces

Pit mud (PM) is among the key factors determining the quality of Nongxiangxing baijiu, a Chinese liquor. Microorganisms present inside PM are crucial for the unique taste and flavor of this liquor. In this study, headspace solid-phase microextraction was used in combination with gas chromatography and high-throughput sequencing to determine the volatile compounds and microbial community structure of 10- and 40-year PM samples from different spaces. The basic physicochemical properties of the PM were also determined. LEfSe and RDA were used to systematically study the PM in different time spaces. The physicochemical properties and ester content of the 40-year PM were higher than those of the 10-year PM, but the spatial distribution of the two years PM samples exhibited no consistency, except in terms of pH, available phosphorus content, and ester content. In all samples, 29 phyla, 276 families, and 540 genera of bacteria, including four dominant phyla and 20 dominant genera, as well as eight phyla, 24 families, and 34 genera of archaea, including four dominant phyla and seven dominant genera, were identified. The LEfSe analysis yielded 18 differential bacteria and five differential archaea. According to the RDA, the physicochemical properties and ethyl caproate, ethyl octanoate, hexanoic acid, and octanoic acid positively correlated with the differential microorganisms of the 40-year PM, whereas negatively correlated with the differential microorganisms of the 10-year PM. Thus, we inferred that Caproiciproducens, norank_f__Caloramatoraceae, and Methanobrevibacter play a dominant and indispensable role in the PM. This study systematically unveils the differences that affect the quality of PM in different time spaces and offers a theoretical basis for improving the declining PM, promoting PM aging, maintaining cellars, and cultivating an artificial PM at a later stage.

Structural biology of microbial gas vesicles: historical milestones and current knowledge

Gas vesicles mediate buoyancy-based motility in aquatic bacteria and archaea and are the only protein-based structures known to enclose a gas-filled volume. Their unique physicochemical properties and ingenious architecture rank them among the most intriguing macromolecular assemblies characterised to date. This review covers the 60-year journey in quest for a high-resolution structural model of gas vesicles, first highlighting significant strides made in establishing the detailed ultrastructure of gas vesicles through transmission electron microscopy, X-ray fibre diffraction, atomic force microscopy, and NMR spectroscopy. We then survey the recent progress in cryogenic electron microscopy studies of gas vesicles, which eventually led to a comprehensive atomic model of the mature assembly. Synthesising insight from these structures, we examine possible mechanisms of gas vesicle biogenesis and growth, presenting a testable model to guide future experimental work. We conclude by discussing future directions in the structural biology of gas vesicles, particularly considering advancements in AI-driven structure prediction.

Soil warming increases the number of growing bacterial taxa but not their growth rates

Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.

Climate and local environment co-mediate the taxonomic and functional diversity of bacteria and archaea in the Qinghai-Tibet Plateau rivers

Understanding the environmental response patterns of riverine microbiota is essential for predicting the potential impact of future environmental change on river ecosystems. Vulnerable plateau ecosystems are particularly sensitive to climate and local environmental changes, however, the environmental response patterns of the taxonomic and functional diversity of riverine microbiota remain unclear. Here, we conducted a systematic investigation of the taxonomic and functional diversity of bacteria and archaea from riparian soils, sediments, and water across the elevation of 1800- 4800 m in the Qinghai-Tibet Plateau rivers. We found that within the elevation range of 1800 to 3800 m, riparian soils and sediments exhibited similarities and stabilities in microbial taxonomic and functional diversity, and water microbiomes were more sensitive with great fluctuations in microbial diversity. Beyond the elevation of 3800 m, microbial diversity declined across all riverine matrixes. Local environmental conditions can influence the sensitivity of microbiomes to climate change. The combination of critical climate and local environmental factors, including total nitrogen, total organic carbon, as well as climate variables associated with temperature and precipitation, provided better explanations for microbial diversity than single-factor analyses. Under the extremely adverse scenario of high greenhouse gas emission concentrations (SSP585), we anticipate that by the end of this century, the bacterial, archaeal, and microbial functional diversity across the river network of the Yangtze and Yellow source basin would potentially change by -16.9- 5.2 %, -16.1- 5.7 %, and -9.3- 6.4 %, respectively. Overall, climate and local environments jointly shaped the microbial diversity in plateau river ecosystems, and water microbiomes would provide early signs of environmental changes. Our study provides effective theoretical foundations for the conservation of river biodiversity and functional stability under environmental changes.

Assessing the effectiveness of 3, 4-dimethylpyrazole phosphate (DMPP) inhibitor in mitigating N2O emissions from contrasting Cd-contaminated soils

Improving nitrogen use efficiency of chemical fertilizers is essential to mitigate the negative environmental impacts of nitrogen. Nitrification, the conversion of ammonium to nitrate via nitrite by soil microbes, is a prominent source of nitrogen loss in soil systems. The effectiveness of nitrification inhibitors in reducing nitrogen loss through inhibition of nitrification is well-documented, however, their efficacy in heavy metals-contaminated soils needs thorough investigations. The current study assessed the efficacy of nitrification inhibitor 3, 4-dimethylpyrazole phosphate (DMPP) in reducing nitrous oxide (N2O) emissions in cadmium (Cd) contaminated paddy and red soils under lab-controlled environment. Obtained results indicated the substantial reduction in N2O emissions with DMPP in paddy and red soil by 48 and 35 %, respectively. However, Cd contamination resulted in reduced efficacy of DMPP, thus decreased the N2O emissions by 36 and 25 % in paddy and red soil, respectively. It was found that addition of DMPP had a significant effect on the abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA). Notably, the reduction in N2O emissions by DMPP varied with the abundance of AOB. Moreover, Cd pollution resulted in a significant (P < 0.05) reduction in the abundance of archaeal and bacterial amoA genes, as well as bacterial nirK, nirS, and nosZ genes. The combined treatment of Cd and DMPP had a detrimental impact on denitrifiers, thereby influencing the overall efficiency of DMPP. These findings provide novel insights into the application of DMPP to mitigate nitrification and its potential role in reducing N2O emissions in contaminated soils.

Unraveling assemblage of microbial community dwelling in Dabaoshan As/Pb/Zn mine-impacted area: A typical mountain mining area of South China

Microbial community assemblage includes microorganisms from the three domains including Bacteria, Archaea, and Eukarya (Fungi), which play a crucial role in geochemical cycles of metal(loid)s in mine tailings. Mine tailings harbor vast proportions of metal(loid)s, representing a unique source of co-contamination of metal(loid)s that threaten the environment. The elucidation of the assembly patterns of microbial communities in mining-impacted ecospheres has received little attention. To decipher the microbial community assembly processes, the microbial communities from the five sites of the Dabaoshan mine-impacted area were profiled by the MiSeq sequencing of 16S rRNA (Bacteria and Archaea) genes and internal transcribed spacers (Fungi). Results indicated that the coexistence of 31 bacterial, 10 fungal, and 3 archaeal phyla, were mainly dominated by Mucilaginibacter, Cladophialophora, and Candidatus Nitrosotalea, respectively. The distribution of microorganisms was controlled by deterministic processes. The combination of Cu, Pb, and Sb was the main factor explaining the structure of microbial communities. Functional predicting analysis of bacteria and archaea based on the phylogenetic investigation of communities by reconstruction of unobserved states analyses revealed that the metabolic pathways related to arsenite transporter, arsenate reductase, and FeS cluster were important for metal detoxification. Furthermore, the ecological guilds (pathogens, symbiotrophs, and saprotrophs) of fungal communities explained 44.5 % of functional prediction. In addition, metal-induced oxidative stress may be alleviated by antioxidant enzymes of fungi communities, such as catalase. Such information provides new insights into the microbial assembly rules in co-contaminated sites.

Streptomyces cathayae sp. nov., an endophytic actinobacterium from the root tissue of Cathaya argyrophylla

An endophytic actinobacterium, designated strain HUAS 5T, was isolated from the root tissue of Cathaya argyrophylla collected in Chenzhou city of Hunan Province, PR China. This strain produced grey aerial mycelium that differentiated into spiral spore chains with spiny-surfaced ellipsoidal spores on Gause's synthetic No. 1 medium. Strain HUAS 5T grew well on Gause's synthetic No. 1, Reasoner'2 and ISP serial media. This strain grew at 15-40 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0) and in presence of 0-5.0% (w/v) NaCl. The predominant cellular fatty acids of strain HUAS 5T (> 5.0%) were iso-C16:0, iso-C14:0, anteiso-C15:0, iso-C15:0, C16:0, iso-C16:1 H and Sum in Feature 3 (C16:1 ω7c/C16:1 ω6c). Sequence analysis of the 16S rRNA gene indicated that this strain belonged to the genus Streptomyces and exhibited highest sequence similarity to Streptomyces hirsutus NRRL B-2713T (97.3%), which is much less than 98.7% cut-off point of species definitions for bacteria and archaea. Phylogenetic analysis of 16S rRNA gene sequence and whole genome indicated that strain HUAS 5T formed an independent lineage, which suggested that it belonged to a potential novel species. Based on the morphological, cultural, physio-biochemical properties and chemotaxonomy, strain HUAS 5T (= MCCC 1K08552T = JCM 36055T) is deemed to represent a novel Streptomyces species, for which we put forward the name Streptomyces cathayae sp. nov.

Cytidine Acetylation Across the Tree of Life

ConspectusAcetylation plays a critical role in regulating eukaryotic transcription via the modification of histones. Beyond this well-documented function, a less explored biological frontier is the potential for acetylation to modify and regulate the function of RNA molecules themselves. N4-Acetylcytdine (ac4C) is a minor RNA nucleobase conserved across all three domains of life (archaea, bacteria, and eukarya), a conservation that suggests a fundamental role in biological processes. Unlike many RNA modifications that are controlled by large enzyme families, almost all organisms catalyze ac4C using a homologue of human Nat10, an essential disease-associated acetyltransferase enzyme.A critical step in defining the fundamental functions of RNA modifications has been the development of methods for their sensitive and specific detection. This Account describes recent progress enabling the use of chemical sequencing reactions to map and quantify ac4C with single-nucleotide resolution in RNA. To orient readers, we first provide historical background of the discovery of ac4C and the enzymes that catalyze its formation. Next, we describe mechanistic experiments that led to the development of first- and second-generation sequencing reactions able to determine ac4C's position in a polynucleotide by exploiting the nucleobase's selective susceptibility to reduction by hydride donors. A notable feature of this chemistry, which may serve as a prototype for nucleotide resolution RNA modification sequencing reactions more broadly, is its ability to drive a penetrant and detectable gain of signal specifically at ac4C sites. Emphasizing practical applications, we present how this optimized chemistry can be integrated into experimental workflows capable of sensitive, transcriptome-wide analysis. Such readouts can be applied to quantitatively define the ac4C landscape across the tree of life. For example, in human cell lines and yeast, this method has uncovered that ac4C is highly selective, predominantly occupying dominant sites within rRNA (rRNA) and tRNA (tRNA). By contrast, when we extend these analyses to thermophilic archaea they identify the potential for much more prevalent patterns of cytidine acetylation, leading to the discovery of a role for this modification in adaptation to environmental stress. Nucleotide resolution analyses of ac4C have also allowed for the determination of structure-activity relationships required for short nucleolar RNA (snoRNA)-catalyzed ac4C deposition and the discovery of organisms with unexpectedly divergent tRNA and rRNA acetylation signatures. Finally, we share how these studies have shaped our approach to evaluating novel ac4C sites reported in the literature and highlight unanswered questions and new directions that set the stage for future research in the field.

Microbial community of municipal drinking water in Hangzhou using metagenomic sequencing

While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaea, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were non-culturable using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the phyla Proteobacteria and Planctomycetes. Notably, the genus Methylobacterium was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp. Archaeal DNA (Euryarchaeota, Crenarchaeota) was found in trace amounts in some DW samples. Viruses such as rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2 were negative in all DW samples using colloidal gold and real-time reverse transcription polymerase chain reaction (RT‒PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (Ortervirales) and Herpesvirales was found in some DW samples. The metabolic pathways of the entire microbial community involve cell‒cell communication and signal secretion, contributing to cooperation between different microbial populations in the water. This study provides insight into the microbial community and metabolic process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.

Host range and cell recognition of archaeal viruses

Archaea are members of a separate domain of life that have unique properties, such as the composition of their cell walls and the structure of their lipid bilayers. Consequently, archaeal viruses face different challenges to infect host cells in comparison with viruses of bacteria and eukaryotes. Despite their significant impact on shaping microbial communities, our understanding of infection processes of archaeal viruses remains limited. Several receptors used by archaeal viruses to infect cells have recently been identified. The interactions between viruses and receptors are one of the determinants of the host range of viruses. Here, we review the current literature on host ranges of archaeal viruses and factors that might impact the width of these host ranges.

Was hydrogen peroxide present before the arrival of oxygenic photosynthesis? The important role of iron(II) in the Archean ocean

We address the chemical/biological history of H2O2 back at the times of the Archean eon (2.5-3.9 billion years ago (Gya)). During the Archean eon the pO2 was million-fold lower than the present pO2, starting to increase gradually from 2.3 until 0.6 Gya, when it reached ca. 0.2 bar. The observation that some anaerobic organisms can defend themselves against O2 has led to the view that early organisms could do the same before oxygenic photosynthesis had developed at about 3 Gya. This would require the anaerobic generation of H2O2, and here we examine the various mechanisms which were suggested in the literature for this. Given the concentration of Fe2+ at 20-200 μM in the Archean ocean, the estimated half-life of H2O2 is ca. 0.7 s. The oceanic H2O2 concentration was practically zero. We conclude that early organisms were not exposed to H2O2 before the arrival of oxygenic photosynthesis.

The oral microbiome: diversity, biogeography and human health

The human oral microbiota is highly diverse and has a complex ecology, comprising bacteria, microeukaryotes, archaea and viruses. These communities have elaborate and highly structured biogeography that shapes metabolic exchange on a local scale and results from the diverse microenvironments present in the oral cavity. The oral microbiota also interfaces with the immune system of the human host and has an important role in not only the health of the oral cavity but also systemic health. In this Review, we highlight recent advances including novel insights into the biogeography of several oral niches at the species level, as well as the ecological role of candidate phyla radiation bacteria and non-bacterial members of the oral microbiome. In addition, we summarize the relationship between the oral microbiota and the pathology of oral diseases and systemic diseases. Together, these advances move the field towards a more holistic understanding of the oral microbiota and its role in health, which in turn opens the door to the study of novel preventive and therapeutic strategies.

Mathematical modeling and experimental validation of a novel Circulating Oxygenation Biofilm Equipment (COBE) for the management of decentralized wastewater treatment

The difficulties of management were the key barriers to the promotion of decentralized wastewater treatment in remote areas. In this study, a novel decentralized Circulating Oxygenation Biofilm Equipment (COBE) and its remote management potential based on mathematical modeling were investigated. The COBE is an integrated biofilm reactor that employs drippage aeration and enables oxygenation, filtration, and effluent processes to be controlled, thus providing convenience for controlling. The model for the COBE describing drippage aeration, comprehensive ammonia-related microbes, and corncob carbon source release process was studied to uncover the impacts of operational conditions on decentralized wastewater treatment in the COBE system. The equipment regulation parameter (circulating oxygenation ratio) was found to be linearly correlated with the oxygen mass transfer coefficient. This discovery enabled highly accurate prediction of COD, NH4-N, and TN concentrations in the equipment effluent at various scenarios. The comprehensive ammonia oxidation biological model indicated that the model could duplicate the actual situation of the succession of ammonia metabolizing related microorganisms. Comammox and ammonia-oxidizing archaea (AOA) dominated ammonia metabolism in this equipment rather than conventional ammonium-oxidizing bacteria (AOB). This study could contribute to the Internet of Things system construction of decentralized wastewater treatment equipment, and provide a solution for timely decentralized equipment management in remote areas.

Modulation of Host Physiology and Pathophysiology by the Gut Microbiome

The human gut microbiome is a highly dynamic community of bacteria, fungi, viruses, archaea, and protozoans that resides within the gastrointestinal tract [...].

Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions

BACKGROUND

Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains.

RESULTS

Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization.

CONCLUSIONS

We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.

Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius

Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.

Microbial diversity and community structure dynamics in acid mine drainage: Acidic fire with dissolved heavy metals

Acid mine drainage (AMD) is one of the leading causes of environmental pollution and is linked to public health and ecological consequences. Microbes-mineral interaction generates AMD, but microorganisms can also remedy AMD pollution. Exploring the microbial response to AMD effluents may reveal survival strategies in extreme ecosystems. Three distinct sites across a mine (inside the mine, the entrance of the mine, and outside) were selected to study their heavy metal concentrations due to significant variations in pH and physicochemical characteristics, and high-throughput sequencing was carried out to investigate the microbial diversity. The metal and ion concentrations followed the order SO42-, Fe, Cu, Zn, Mg, Pb, Co, Cr, and Ni from highest to lowest, respectively. Maximum sequences were allocated to Proteobacteria and Firmicutes. Among archaea, the abundance of Thaumarchaeota and Euryarchaeota was higher outside of mine. Most of the genera (23.12 %) were unclassified and unknown. The average OTUs (operational taxonomic units) were significantly higher outside the mine; however, diversity indices were not significantly different across the mine sites. Hierarchical clustering of selective genera and nMDS ordination of OTUs displayed greater segregation resolution inside and outside of mine, whereas the entrance samples clustered with greater similarity. Heterogeneous selection might be the main driver of community composition outside the mine, whereas stochastic processes became prominent inside the mine. However, the ANOSIM test shows a relatively even distribution of community composition within and between the groups. Microbial phyla showed both positive and negative correlations with physicochemical factors. A greater number of biomarkers were reported outside of the mine. Predictive functional investigation revealed the existence of putative degradative, metabolic, and biosynthetic pathways. This study presents a rare dataset in our understanding of microbial diversity and distribution as shaped by the ecological gradient and potential novelty in phylogenetic/taxonomic diversity in AMD, with potential biotechnological applications.

A Versatile Aldehyde: Ferredoxin Oxidoreductase from the Organic Acid Reducing Thermoanaerobacter sp. Strain X514

Aldehyde:ferredoxin oxidoreductases (AORs) have been isolated and biochemically-characterized from a handful of anaerobic or facultative aerobic archaea and bacteria. They catalyze the ferredoxin (Fd)-dependent oxidation of aldehydes to acids. Recently, the involvement of AOR in the reduction of organic acids to alcohols with electrons derived from sugar or synthesis gas was demonstrated, with alcohol dehydrogenases (ADHs) carrying out the reduction of the aldehyde to the alcohol (AOR-ADH pathway). Here, we describe the biochemical characterization of an AOR of the thermophilic fermentative bacterium Thermoanaerobacter sp. strain X514 (AORX514). The putative aor gene (Teth514_1380) including a 6x-His-tag was introduced into the genome of the genetically-accessible, related species Thermoanaerobacter kivui. The protein was purified to apparent homogeneity, and indeed revealed AOR activity, as measured by acetaldehyde-dependent ferredoxin reduction. AORX514 was active over a wide temperature (10 to 95 °C) and pH (5.5 to 11.5) range, utilized a wide variety of aldehydes (short and branched-chained, aliphatic, aromatic) and resembles archaeal sensu stricto AORs, as the protein is active in a homodimeric form. The successful, recombinant production of AORX514 in a related, well-characterized and likewise strict anaerobe paves the road towards structure-function analyses of this enzyme and possibly similar oxygen-sensitive or W/Mo-dependent proteins in the future.

Discrepant assembly processes of prokaryotic communities between the abyssal and hadal sediments in Yap Trench

Abyssal and hadal sediments represent two of the most type ecosystems on Earth and have the potential interactions with geochemistry. However, little is known about the prokaryotic community assembly and the response of prokaryotic communities to metal(loid)s in trench sediments due to the lack of adequate and appropriate samples. In this study, a systematic investigation combined the assembly mechanisms and co-occurrence patterns of prokaryotic communities between the hadal and abyssal sediments across the Yap Trench. The results revealed that the hadal prokaryotes had less species diversity, but more abundant function than the abyssal prokaryotes. The prokaryotic communities in the abyssal sediments had more core taxa than the hadal sediments. Twenty-one biomarkers mostly affiliated with Nitrosopumilaceae were detected using Random-Forests machine learning algorithm. Furthermore, stochasticity was dominant in the prokaryotic community assembly processes of the Yap Trench sediments. Meanwhile, homogeneous selection (32.6%-52.9%) belonging to deterministic processes governed the prokaryotic community assembly in hadal sediments with increasing of sediment depth. In addition to total nitrogen and total organic carbon, more metal(loid)s were significantly correlated with the prokaryotic community in the hadal sediments than that in the abyssal sediments. The hadal prokaryotic communities was most positively related to bismuth (r = 0.31, p < 0.01), followed by calcium, chromium, cerium, potassium, plumbum, scandium, titanium, and vanadium. Finally, co-occurrence networks revealed two potential dominant prokaryotic modules in Yap Trench sediments covaried across oceanographic zonation. By contrast, the hadal network had relatively more complexity, more bacterial taxa, and more associations among prokaryotic taxa, relative to the abyssal network. This study reveals potentially metal variables and community assembly mechanisms of the prokaryotic community in abyssal and hadal sediments and provides a better understanding on the prokaryotic diversity and ecology in trench sediment ecosystems.

Effects of microplastics on cold seep sediment prokaryotic communities

Cold seep sediments are an important reservoir of microplastics (MPs) whose impact on the structure and function of prokaryotic community is not well understood. In this study, the impact of 0.2% and 1% (w/w) polyethylene (PE), polystyrene (PS), and polypropylene (PP) MPs on the cold seep sediment prokaryotic community was investigated in a 120-day laboratory incubation experiment. The results revealed that exposure to MPs altered sedimentary chemical properties in a type- and concentration-dependent manner. Furthermore, MPs significantly altered the structure of bacterial community, with some MPs degradation-associated bacterial phyla significantly increasing (p < 0.05). However, in the case of archaea, the changes in the structure of microbial community were less pronounced (p > 0.05). Co-occurrence network analysis revealed that the addition of MPs reduced the network complexity, while PICRUSt2 and FAPROTAX analyses suggested that 0.2% PP and 1% PS MPs had the most significant effects on the nitrogen and carbon cycles (p < 0.05). Overall, this study provides new insights into the effects of MPs on the structure and function of microbial communities in cold seep sediments.

Soil amendments promoting nitrifying bacteria recovery faster than the denitrifying bacteria at post soil fumigation

Chloropicrin (CP) is a soil fumigant that not only reduces disease-causing pathogenic microbes but regrettably also those that benefit soil quality and crop health. However, we have few knowledge on rapidly restoring populations of beneficial microbes suppressed by CP fumigation. Here we used genetic sequencing technology to monitor changes in the recovery of soil bacteria in response to ammonium sulfate added to the soil following CP fumigation. The results showed that regardless of the N fertilizer addition rate, the accumulated NH4+-N in CP fumigated soil was rapidly consumed within 42 d. The rapid reduction in NH4+-N coincided with the observed recovery nitrogen-cycling microorganisms, especially the nitrification bacteria AOA and AOB that contributed to the formation of NH4+-N. Additionally, we further observed that the resilience index of nitrifying bacteria (AOB and AOA) was greater than the resilience index of denitrifying bacteria that contain the denitrification genes nirS, nirK and nosZ (0.12 to 0.55 vs. -0.27 to 0.073). These results revealed that N fertilizer stimulated the recovery of nitrifying bacteria more than denitrifying bacteria. Our research suggests that ammonium sulfate applied to CP fumigated soil could be used commercially to improve soil health as a result of an increase in beneficial microbes.