Predominance of Cand. Patescibacteria in Groundwater Is Caused by Their Preferential Mobilization From Soils and Flourishing Under Oligotrophic Conditions

Genome streamlining in Parcubacteria transitioning from soil to groundwater

BACKGROUND

To better understand the influence of habitat on the genetic content of bacteria, with a focus on members of Candidate Phyla Radiation (CPR) bacteria, we studied the effects of transitioning from soil via seepage waters to groundwater on genomic composition of ultra-small Parcubacteria, the dominating CPR class in seepage waters, using genome resolved metagenomics.

RESULTS

Bacterial metagenome-assembled genomes (MAGs), (318 total, 32 of Parcubacteria) were generated from seepage waters and compared directly to groundwater counterparts. The estimated average genome sizes of members of major phyla Proteobacteria, Bacteroidota and Cand. Patescibacteria (Candidate Phyla Radiation - CPR bacteria) were significantly higher in soil-seepage water as compared to their groundwater counterparts. Seepage water Parcubacteria (Paceibacteria) exhibited 1.18-fold greater mean genome size and 2-fold lower mean proportion of pseudogenes than those in groundwater. Bacteroidota and Proteobacteria also showed a similar trend of reduced genomes in groundwater compared to seepage. While exploring gene loss and adaptive gains in closely related CPR lineages in groundwater, we identified a membrane protein, and a lipoglycopeptide resistance gene unique to a seepage Parcubacterium genome. A nitrite reductase gene was also identified and was unique to the groundwater Parcubacteria genomes, likely acquired from other planktonic microbes via horizontal gene transfer.

CONCLUSIONS

Overall, our data suggest that bacteria in seepage waters, including ultra-small Parcubacteria, have significantly larger genomes and higher metabolic enrichment than their groundwater counterparts, highlighting possible genome streamlining of the latter in response to habitat selection in an oligotrophic environment.

Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere

Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.

Effect of tire wear particle accumulation on nitrogen removal and greenhouse gases abatement in bioretention systems: Soil characteristics, microbial community, and functional genes

Tire wear particles (TWPs), as predominant microplastics (MPs) in road runoff, can be captured and retained by bioretention systems (BRS). This study aimed to investigate the effect of TWPs accumulation on nitrogen processes, focusing on soil characteristics, microbial community, and functional genes. Two groups of lab-scale bioretention columns containing TWPs (0 and 100 mg g-1) were established. The removal efficiencies of NH4+-N and TN in BRS significantly decreased by 7.60%-24.79% and 1.98%-11.09%, respectively, during the 101 days of TWPs exposure. Interestingly, the emission fluxes of N2O and CO2 were significantly decreased, while the emission flux of CH4 was substantially increased. Furthermore, prolonged TWPs exposure significantly influenced the contents of soil organic matter (increased by 27.07%) and NH4+-N (decreased by 42.15%) in the planting layer. TWPs exposure also significantly increased dehydrogenase activity and substrate-induced respiration rate, thereby promoting microbial metabolism. Microbial sequencing results revealed that TWPs decreased the relative abundance of nitrifying bacteria (Nitrospira and Nitrosomonas) and denitrifying bacteria (Dechloromonas and Thauera), reducing the nitrification rate by 42.24%. PICRUSt2 analysis further indicated that TWPs changed the relative abundance of functional genes related to nitrogen and enzyme-coding genes.

Antimicrobial resistance in rural rivers: Comparative study of the Coquet (Northumberland) and Eden (Cumbria) River catchments

Many studies have characterised resistomes in river microbial communities. However, few have compared resistomes in parallel rural catchments that have few point-source inputs of antimicrobial genes (ARGs) and organisms (i.e., AMR) - catchments where one can contrast more nebulous drivers of AMR in rural rivers. Here, we used quantitative microbial profiling (QMP) to compare resistomes and microbiomes in two rural river catchments in Northern England, the Coquet and Eden in Northumberland and Cumbria, respectively, with different hydrological and geographical conditions. The Eden has higher flow rates, higher annual surface runoff, and longer periods of soil saturation, whereas the Coquet is drier and has lower flowrates. QMP analysis showed the Eden contained significantly more abundant microbes associated with soil sources, animal faeces, and wastewater than the Coquet, which had microbiomes like less polluted rivers (Wilcoxon test, p < 0.01). The Eden also had greater ARG abundances and resistome diversity (Kruskal Wallis, p < 0.05), and higher levels of potentially clinically relevant ARGs. The Eden catchment had greater and flashier runoff and more extensive agricultural land use in its middle reach, which explains higher levels of AMR in the river. Hydrological and geographic factors drive AMR in rural rivers, which must be considered in environmental monitoring programmes.

Experimental research on the transport-transformation of organic contaminants under the influence of multi-field coupling at a site scale

Organic-contaminated shallow aquifers have become a global concern of groundwater contamination, yet little is known about the coupled effects of hydrodynamic-thermal-chemical-microbial (HTCM) multi-field on organic contaminant transport and transformation over a short time in aquifers. Therefore, this study proposed a quick and efficient field experimental method for the transport-transformation of contaminants under multi-field coupling to explore the relationship between organic contaminants (total petroleum hydrocarbon (TPH), polycyclic aromatic hydrocarbons (PAHs), benzene-toluene-ethylbenzene-xylene (BTEX) and phthalates acid esters (PAEs)) and multi-field factors. The results showed that hydrodynamics (affecting pH, p < 0.001) and temperature (affecting dissolved oxygen, pH and HCO3-, p < 0.05) mainly affected the organic contaminants indirectly by influencing the hydrochemistry to regulate redox conditions in the aquifer. The main degradation reactions of the petroleum hydrocarbons (TPH, PAHs and BTEX) and PAEs in the aquifer were sulfate reduction and nitrate reduction, respectively. Furthermore, the organic contamination was directly influenced by microbial communities, whose spatial patterns were shaped by the combined effects of the spatial pattern of hydrochemistry (induced by the organic contamination pressure) and other multi-field factors. Overall, our findings imply that the spatiotemporal patterns of organic contaminants are synergistically regulated by HTCM, with distinct mechanisms for petroleum hydrocarbons and PAEs.

Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode

Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.

Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures

Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.

Exploratory study on the metabolic similarity of denitrifying carbon sources

Mixed carbon sources have been developed for denitrification to eliminate the "carbon dependency" problem of single carbon. The metabolic correlation between different carbon sources is significant as guidance for the development of novel mixed carbon sources. In this study, to explore the metabolic similarity of denitrifying carbon sources, we selected alcohols (methanol, ethanol, and glycerol) and saccharide carbon sources (glucose, sucrose, and starch). Batch denitrification experiments revealed that methanol-acclimated sludge improved the denitrification rate of both methanol (14.42 mg-N/gMLVSS*h) and ethanol (9.65 mg-N/gMLVSS*h), whereas ethanol-acclimated sludge improved the denitrification rate of both methanol (7.80 mg-N/gMLVSS*h) and ethanol (22.23 mg-N/gMLVSS*h). In addition, the glucose-acclimated sludge and sucrose-acclimated sludge possibly improved the denitrification rate of glucose and sucrose, and the glycerol-acclimated sludge improved the denitrification rate of volatile fatty acids (VFAs), alcohols, and saccharide carbon sources. Functional gene analysis revealed that methanol, ethanol, and glycerol exhibited active alcohol oxidation and glyoxylate metabolism, and glycerol, glucose, and sucrose exhibited active glycolysis metabolism. This indicated that the similarity in the denitrification metabolism of these carbon sources was based on functional gene similarity, and glycerol-acclimated sludge exhibited the most diverse metabolism, which ensured its good denitrification effect with other carbon sources.

Assessing the impact of three feeding stages on rumen bacterial community and physiological characteristics of Japanese Black cattle

In Japan, Japanese Black cattle, known for their exceptional meat quality owing to their abundant intramuscular fat, undergo a unique three-stage feeding system with varying concentrate ratios. There is limited research on physiological and rumen microbial changes in Japanese Black cattle during these stages. Therefore, this study aimed to examine Japanese Black steers in these three stages: early (T1, 12-14 months), middle (T2, 15-22 months), and late (T3, 23-30 months). The rumen bacteria of 21 cattle per phase was analyzed using 16S rRNA gene sequencing. Rumen bacterial diversity was significantly higher in T1, with a distinct distribution, than in T2 and T3. Specific phyla and genera were exclusive to each stage, reflecting the shifts in feed composition. Certain genera dominated each stage: T1 had Flexilinea, Streptococcus, Butyrivibrio, Selenomonas, and Kandleria; T2 had Bifidobacterium, Shuttleworthia, and Sharpea; and T3 had Acetitomaculum, Mycoplasma, Atopobium, and Howardella. Correlation analysis revealed significant associations between certain microbial populations and physiological parameters. These findings indicate that changes in energy content and feed composition are associated with physiological and ruminal alterations. This study may guide strategies to improve rumen health and productivity in Japanese Black cattle by modifying diets to specific fattening stages.

Membrane aerated biofilm reactor system driven by pure oxygen for wastewater treatment

Pure oxygen is proposed for wastewater treatment due to its advantages over conventional air aeration. This study investigates a Pure Oxygen-based Membrane Aerated Biofilm Reactor (PO-MABR) for the first time under various operating conditions. The PO-MABR employs a gas-permeable membrane for direct diffusion of low-pressurized pure oxygen to the biofilm, ensuring exceptional carbon and nitrogen removal. The effectiveness of PO-MABR was investigated by varying operational conditions, including temperature, carbon-to-nitrogen ratio, gas pressure, and flow rate. Results indicate superior performance, with a 97% chemical oxygen demand removal and 19% higher total nitrogen removal than Air-Ventilated MABR (A-MABR) due to thicker biofilm and unique microbial structures in PO-MABR. Also, PO-MABR demonstrated resilience to low temperatures and effectively treated both high and low-strength wastewater. The findings emphasize the efficiency of PO-MABR in wastewater treatment, advocating for its adoption due to superior carbon and nitrogen removal across diverse operational conditions.

Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.

Microbial dark matter sequences verification in amplicon sequencing and environmental metagenomics data

Although microorganisms constitute the most diverse and abundant life form on Earth, in many environments, the vast majority of them remain uncultured. As it is based on information gleaned mainly from cultivated microorganisms, our current body of knowledge regarding microbial life is partial and does not reflect actual microbial diversity. That diversity is hidden in the uncultured microbial majority, termed by microbiologists as "microbial dark matter" (MDM), a term borrowed from astrophysics. Metagenomic sequencing analysis techniques (both 16S rRNA gene and shotgun sequencing) compare gene sequences to reference databases, each of which represents only a small fraction of the existing microorganisms. Unaligned sequences lead to groups of "unknown microorganisms" that are usually ignored and rarefied from diversity analysis. To address this knowledge gap, we analyzed the 16S rRNA gene sequences of microbial communities from four different environments-a living organism, a desert environment, a natural aquatic environment, and a membrane bioreactor for wastewater treatment. From those datasets, we chose representative sequences of potentially unknown bacteria for additional examination as "microbial dark matter sequences" (MDMS). Sequence existence was validated by specific amplification and re-sequencing. These sequences were screened against databases and aligned to the Genome Taxonomy Database to build a comprehensive phylogenetic tree for additional sequence classification, revealing potentially new candidate phyla and other lineages. These putative MDMS were also screened against metagenome-assembled genomes from the explored environments for additional validation and for taxonomic and metabolic characterizations. This study shows the immense importance of MDMS in environmental metataxonomic analyses of 16S rRNA gene sequences and provides a simple and readily available methodology for the examination of MDM hidden behind amplicon sequencing results.

Tributary Inflows to a Regulated River Influence Bacterial Communities and Increase Bacterial Carbon Assimilation

Inflows from unregulated tributaries change the physical, chemical, and biotic conditions in receiving regulated rivers, impacting microbial community structure and metabolic function. Understanding how tributary inflows affect bacterial carbon production (BCP) is integral to understanding energy transfer in riverine ecosystems. To investigate the role of tributary inflows on bacterial community composition and BCP, a ~90th percentile natural flow event was sampled over 5 days along the Lachlan River and its tributaries within the Murray-Darling Basin of eastern Australia. Increased tributary inflows after rainfall corresponded with a significantly different and more diverse bacterial community in the regulated mainstem. The major contributor to this difference was an increase in relative abundance of bacterial groups with a potential metabolic preference for humic substances (Burkholderiaceae Polynucleobacter, Alcaligenaceae GKS98 freshwater group, Saccharimonadia) and a significant decrease in Spirosomaceae Pseudarcicella, known to metabolise algal exudates. Increases in orthophosphate and river discharge explained 31% of community change, suggesting a combination of resource delivery and microbial community coalescence as major drivers. BCP initially decreased significantly with tributary inflows, but the total load of carbon assimilated by bacteria increased by up to 20 times with flow due to increased water volume. The significant drivers of BCP were dissolved organic carbon, water temperature, and conductivity. Notably, BCP was not correlated with bacterial diversity or community composition. Tributary inflows were shown to alter mainstem bacterial community structure and metabolic function to take advantage of fresh terrestrial dissolved organic material, resulting in substantial changes to riverine carbon assimilation over small times scales.

Co-application of chitooligosaccharides and arbuscular mycorrhiza fungi reduced greenhouse gas fluxes in saline soil by improving the rhizosphere microecology of soybean

Soil salinization can affect the ecological environment of soil and alter greenhouse gas (GHG) emissions. Chitooligosaccharides and Arbuscular mycorrhizal fungi (AMF) reduced the GHG fluxes of salinized soil, and this reduction was attributed to an alteration in the rhizosphere microecology, including changes in the activities of β-glucosidase, acid phosphatase, N-acetyl-β-D-glucosidase, and Leucine aminopeptidase. Additionally, certain bacteria species such as paracoccus, ensifer, microvirga, and paracyclodium were highly correlated with GHG emissions. Another interesting finding is that foliar spraying of chitooligosaccharides could transport to the soybean root system, and improve soybean tolerance to salt stress. This is achieved by enhancing the activities of antioxidant enzymes, and the changes in amino acid metabolism, lipid metabolism, and membrane transport. Importantly, the Co-application of chitooligosaccharides and Arbuscular mycorrhiza fungi was found to have a greater effect compared to their application alone.

New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain)

In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.

Microbial communities in paddy soils: differences in abundance and functionality between rhizosphere and pore water, the influence of different soil organic carbon, sulfate fertilization and cultivation time, and contribution to arsenic mobility and speciation

Abiotic factors and rhizosphere microbial populations influence arsenic accumulation in rice grains. Although mineral and organic surfaces are keystones in element cycling, localization of specific microbial reactions in the root/soil/pore water system is still unclear. Here, we tested if original unplanted soil, rhizosphere soil and pore water represented distinct ecological microniches for arsenic-, sulfur- and iron-cycling microorganisms and compared the influence of relevant factors such as soil type, sulfate fertilization and cultivation time. In rice open-air-mesocosms with two paddy soils (2.0% and 4.7% organic carbon), Illumina 16S rRNA gene sequencing demonstrated minor effects of cultivation time and sulfate fertilization that decreased Archaea-driven microbial networks and incremented sulfate-reducing and sulfur-oxidizing bacteria. Different compartments, characterized by different bacterial and archaeal compositions, had the strongest effect, with higher microbial abundances, bacterial biodiversity and interconnections in the rhizosphere vs pore water. Within each compartment, a significant soil type effect was observed. Higher percentage contributions of rhizosphere dissimilatory arsenate- and iron-reducing, arsenite-oxidizing, and, surprisingly, dissimilatory sulfate-reducing bacteria, as well as pore water iron-oxidizing bacteria in the lower organic carbon soil, supported previous chemistry-based interpretations of a more active S-cycling, a higher percentage of thioarsenates and lower arsenic mobility by sorption to mixed Fe(II)Fe(III)-minerals in this soil.

A glimpse of the paleome in endolithic microbial communities

BACKGROUND

The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.

RESULTS

By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 105 cells × g-1 rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.

CONCLUSIONS

Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.

Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment

Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms. However, most insights into this group come from a surprisingly small number of environments, and recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. In this study we enriched soil samples from 14 different soil fertility treatments for ultra-small (<0.45 μm) bacteria in order to study rare soil CPR. 42 samples were sequenced, enabling the reconstruction of 27 quality CPR metagenome-assembled genomes (MAGs) further classified as Parcubacteria/Paceibacteria, Saccharibacteria/Saccharimonadia and ABY1, in addition to representative genomes from Gemmatimonadetes, Dependentiae and Chlamydae phyla. These genomes were fully annotated and used to reconstruct the CPR community across all 14 plots. Additionally, for five of these plots, the entire microbiota was reconstructed using 16S amplification, showing that specific soil CPR may form symbiotic relationships with a varied and circumstantial range of hosts. Cullars CPR had a prevalence of enzymes predicted to degrade plant-derived carbohydrates, which suggests they have a role in plant biomass degradation. Parcubacteria appear to be more apt at microfauna necromass degradation. Cullars Saccharibacteria and a Parcubacteria group were shown to carry a possible aerotolerance mechanism coupled with potential for aerobic respiration, which appear to be a unique adaptation to the oxic soil environment. Reconstruction of CPR communities across treatment plots showed that they were not impacted by changes in nutrient levels or microbiota composition, being only impacted by extreme conditions, causing some CPR to dominate the community. These findings corroborate the understanding that soil-dwelling CPR bacteria have a very broad symbiont range and have metabolic capabilities associated to soil environments which allows them to scavenge resources and form resilient communities. The contributions of these microbial dark matter species to soil ecology and plant interactions will be of significant interest in future studies.

Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater

The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.

Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics

Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.

Effects of dietary N-carbamylglutamate on rumen fermentation parameters, and bacterial community diversity of Holstein dairy cows in Tibet

Introduction

The Tibetan Plateau is characterized by low temperature and hypoxia. N-carbamylglutamic acid (NCG) can increase blood oxygen saturation, and have the potential to be used to prevent the high-altitude hypoxia stress state of cows. However, its beneficial effect on the rumen microbiota of Holstein dairy cows remains unclear.

Methods

Hence, the experiments 12 multiparous (parity ranged from 2 to 7) Holstein dairy cows (413.0 ± 42 kg) were randomly assigned to 2 treatments with 6 replicates in each treatment: basal diet (CON, control group) and basal diet plus 20 g/d/cow of NCG (NCG, experiment group), respectively. To study the effects of dietary NCG supplementation on rumen microbiota of Holstein dairy cows in Tibet. The experiment lasted for 45 days, with 15 days of pre-feeding and 30 days of formal trail period.

Results

The results showed that ruminal NH₃-N concentration in NCG group was lower (p < 0.05) than that in the CON group, while molar proportion of acetic acid and total volatile fatty acid (VFA) concentration were increased (p < 0.05) with the addition of NCG. Microbial diversity increased (p < 0.05) in NCG group, with Bacteroidetes, Firmicutes, and Patescibacteria as the most abundant phyla. The KEGG pathway analysis showed that the potential function of ruminal bacteria was mainly enriched in metabolism (carbohydrates, amino acids, lipids, energy, and nucleotides) and genetic information processing (replication, repair, and translation).

Conclusion

In conclusion, NCG can improve rumen nitrogen utilization, total VFA and acetic acid production, and increase rumen microbial diversity, all of which could make the introduced Holstein dairy cows to better adapt to the harsh environment in Tibet and improve their production performance.

Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings

Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.

Monitoring groundwater quality with real-time data, stable water isotopes, and microbial community analysis: A comparison with conventional methods

Groundwater provides much of the world's potable water. Nevertheless, groundwater quality monitoring programmes often rely on a sporadic, slow, and narrowly focused combination of periodic manual sampling and laboratory analyses, such that some water quality deficiencies go undetected, or are detected too late to prevent adverse consequences. In an effort to address this shortcoming, we conducted enhanced monitoring of untreated groundwater quality over 12 months (February 2019-February 2020) in four shallow wells supplying potable water in Finland. We supplemented periodic manual sampling and laboratory analyses with (i) real-time online monitoring of physicochemical and hydrological parameters, (ii) analysis of stable water isotopes from groundwater and nearby surface waters, and (iii) microbial community analysis of groundwater via amplicon sequencing of the 16S rRNA gene and 16S rRNA. We also developed an early warning system (EWS) for detecting water quality anomalies by automating real-time online monitoring data collection, transfer, and analysis - using electrical conductivity (EC) and turbidity as indirect water quality indicators. Real-time online monitoring measurements were largely in fair agreement with periodic manual measurements, demonstrating their usefulness for monitoring water quality; and the findings of conventional monitoring, stable water isotopes, and microbial community analysis revealed indications of surface water intrusion and faecal contamination at some of the studied sites. With further advances in technology and affordability expected into the future, the supplementary methods used here could be more widely implemented to enhance groundwater quality monitoring - by contributing new insights and/or corroborating the findings of conventional analyses.

Ecological landscape explains aquifers microbial structure

Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.

High-throughput sequencing as a tool for monitoring prokaryote communities in a wastewater treatment plant

In this study, the DNA metabarcoding technique was used to explore the prokaryote diversity and community structure in wastewater collected in spring and winter 2020-2021 as well as the efficiency of the treatment in a wastewater treatment plant (WWTP) in Ría de Vigo (NW Spain). The samplings included raw wastewater from the inlet stream (M1), the discharge water after the disinfection treatment (M3) and mussels used as bioindicators of possible contamination of the marine environment. Significant differences were discovered in the microbiome of each type of sample (M1, M3 and mussels), with 92 %, 45 % and 44 % of exclusive OTUs found in mussel, M3 and M1 samples respectively. Seasonal differences were also detected in wastewater samples, with which abiotic parameters (temperature, pH) could be strongly involved. Bacteria present in raw wastewater (M1) were associated with the human gut microbiome, and therefore, potential pathogens that could be circulating in the population in specific periods were detected (e.g., Arcobacter sp. and Clostridium sp.). A considerable decrease in putative pathogenic organisms from the M1 to M3 wastewater fractions and the scarce presence in mussels (<0.5 % total reads) confirmed the effectiveness of pathogen removal in the wastewater treatment plant. Our results showed the potential of the DNA metabarcoding technique for monitoring studies and confirmed its application in wastewater-based epidemiology (WBE) and environmental contamination studies. Although this technique cannot determine if the infective pathogens are present, it can characterize the microbial communities and the putative pathogens that are circulating through the population (microbiome of M1) and also confirm the efficacy of depuration treatment, which can directly affect the aquaculture sector and even human and veterinary health.

Ultra-small bacteria and archaea exhibit genetic flexibility towards groundwater oxygen content, and adaptations for attached or planktonic lifestyles

Aquifers are populated by highly diverse microbial communities, including unusually small bacteria and archaea. The recently described Patescibacteria (or Candidate Phyla Radiation) and DPANN radiation are characterized by ultra-small cell and genomes sizes, resulting in limited metabolic capacities and probable dependency on other organisms to survive. We applied a multi-omics approach to characterize the ultra-small microbial communities over a wide range of aquifer groundwater chemistries. Results expand the known global range of these unusual organisms, demonstrate the wide geographical range of over 11,000 subsurface-adapted Patescibacteria, Dependentiae and DPANN archaea, and indicate that prokaryotes with ultra-small genomes and minimalistic metabolism are a characteristic feature of the terrestrial subsurface. Community composition and metabolic activities were largely shaped by water oxygen content, while highly site-specific relative abundance profiles were driven by a combination of groundwater physicochemistries (pH, nitrate-N, dissolved organic carbon). We provide insights into the activity of ultra-small prokaryotes with evidence that they are major contributors to groundwater community transcriptional activity. Ultra-small prokaryotes exhibited genetic flexibility with respect to groundwater oxygen content, and transcriptionally distinct responses, including proportionally greater transcription invested into amino acid and lipid metabolism and signal transduction in oxic groundwater, along with differences in taxa transcriptionally active. Those associated with sediments differed from planktonic counterparts in species composition and transcriptional activity, and exhibited metabolic adaptations reflecting a surface-associated lifestyle. Finally, results showed that groups of phylogenetically diverse ultra-small organisms co-occurred strongly across sites, indicating shared preferences for groundwater conditions.

Lacticaseibacillus rhamnosus dfa1 Attenuate Cecal Ligation-Induced Systemic Inflammation through the Interference in Gut Dysbiosis, Leaky Gut, and Enterocytic Cell Energy

Despite an uncommon condition, the clinical management of phlegmon appendicitis (retention of the intra-abdominal appendiceal abscess) is still controversial, and probiotics might be partly helpful. Then, the retained ligated cecal appendage (without gut obstruction) with or without oral Lacticaseibacillus rhamnosus dfa1 (started at 4 days prior to the surgery) was used as a representative model. At 5 days post-surgery, the cecal-ligated mice demonstrated weight loss, soft stool, gut barrier defect (leaky gut using FITC-dextran assay), fecal dysbiosis (increased Proteobacteria with reduced bacterial diversity), bacteremia, elevated serum cytokines, and spleen apoptosis without kidney and liver damage. Interestingly, the probiotics attenuated disease severity as indicated by stool consistency index, FITC-dextran assay, serum cytokines, spleen apoptosis, fecal microbiota analysis (reduced Proteobacteria), and mortality. Additionally, impacts of anti-inflammatory substances from culture media of the probiotics were demonstrated by attenuation of starvation injury in the Caco-2 enterocyte cell line as indicated by transepithelial electrical resistance (TEER), inflammatory markers (supernatant IL-8 with gene expression of TLR4 and NF-κB), cell energy status (extracellular flux analysis), and the reactive oxygen species (malondialdehyde). In conclusion, gut dysbiosis and leaky-gut-induced systemic inflammation might be helpful clinical parameters for patients with phlegmon appendicitis. Additionally, the leaky gut might be attenuated by some beneficial molecules from probiotics.

Nitrogen Fertilizer Type and Genotype as Drivers of P Acquisition and Rhizosphere Microbiota Assembly in Juvenile Maize Plants

Phosphorus (P) is an essential nutrient for plant growth and development, as well as an important factor limiting sustainable maize production. Targeted nitrogen (N) fertilization in the form of ammonium has been shown to positively affect Pi uptake under P-deficient conditions compared to nitrate. Nevertheless, its profound effects on root traits, P uptake, and soil microbial composition are still largely unknown. In this study, two maize genotypes F160 and F7 with different P sensitivity were used to investigate phosphorus-related root traits such as root hair length, root diameter, AMF association, and multiple P efficiencies under P limitation when fertilized either with ammonium or nitrate. Ammonium application improved phosphorous acquisition efficiency in the F7 genotype but not in F160, suggesting that the genotype plays an important role in how a particular N form affects P uptake in maize. Additionally, metabarcoding data showed that young maize roots were able to promote distinct microbial taxa, such as arbuscular mycorrhizal fungi, when fertilized with ammonium. Overall, the results suggest that the form of chemical nitrogen fertilizer can be instrumental in selecting beneficial microbial communities associated with phosphorus uptake and maize plant fitness.

Study of antibiotic resistance in freshwater ecosystems with low anthropogenic impact

This study aimed to investigate the bacterial diversity and the background level of antibiotic resistance in two freshwater ecosystems with low anthropogenic impact in order to evaluate the presence of natural antimicrobial resistance in these areas and its potential to spread downstream. Water samples from a pre-Alpine and an Apennine river (Variola and Tiber, respectively) were collected in three different sampling campaigns and bacterial diversity was assessed by 16S sequencing, while the presence of bacteria resistant to five antibiotics was screened using a culturable approach. Overall bacterial load was higher in the Tiber River compared with the Variola River. Furthermore, the study revealed the presence of resistant bacteria, especially the Tiber River showed, for each sampling, the presence of resistance to all antibiotics tested, while for the Variola River, the detected resistance was variable, comprising two or more antibiotics. Screening of two resistance genes on a total of one hundred eighteen bacterial isolates from the two rivers showed that bla_TEM, conferring resistance to β-lactam antibiotics, was dominant and present in ~58 % of isolates compared to only ~9 % for mefA/E conferring resistance to macrolides. Moreover, β-lactam resistance was detected in various isolates showing also resistance to additional antibiotics such as macrolides, aminoglycosides and tetracyclines. These observations would suggest the presence of co-resistant bacteria even in non-anthropogenic environments and this resistance may spread from the environment to humans and/or animals.

Recovery trajectories of the bacterial community at distances in the receiving river under wastewater treatment plant discharge

Microbes in rivers are an important part of the biogeochemical cycle in aquatic ecosystems, and understanding the major factors that influence the composition of microbial communities has an important role in assessing and improving ecosystem functioning. A high-throughput 16 S rRNA gene sequencing technique was employed to sequence bacterial communities in 21 sediment samples and 21 water samples from an urban river WWTP (wastewater treatment plant) discharge. A systematic study of changes in bacterial community composition in downstream river sediment and water was conducted. The study found that compared with the bacterial diversity in the natural upstream area of the wastewater outfall, the bacterial diversity in the sediment lower reaches decreased significantly, while the bacterial abundance and diversity in the water increased significantly. The Mantel test and redundancy analysis showed that the downstream distance and physicochemical properties were significantly related to the succession of bacterial communities in the sediment downstream of the WWTP discharge. Among them, TOC (total organic carbon) was the most important factor affecting the change in the bacterial community in the downstream sediment. The physicochemical properties were significantly correlated with the succession of bacterial communities in the water downstream of the WWTP discharge. Among them, TN (total nitrogen), PO₄^3--P (phosphorus phosphate) and TP (total phosphorus) were the main factors that affected the change in the bacterial community in the downstream water. Key taxa in the co-occurrence network at different distances downstream reflected the depth of the effect of the WWTP effluent on the bacterial community. The bacterial community in the lower reaches of the river sediment showed a strong recovery ability under the influence of pollutants, while the bacterial community in the lower reaches of the river water was difficult to recover under the influence of pollutants. In general, pollutants contained in effluent are the key to changing the composition of bacterial communities in the lower reaches of the river, but exogenous bacteria in effluent are not. This study provides a basis for further improving the effluent discharge standards of WWTPs in the future.

Effect of Energy Provision Strategy on Rumen Fermentation Characteristics, Bacterial Diversity and Community Composition

This study was conducted to explore the rumen fermentation characteristics, bacterial diversity, and community composition of Hu sheep under four energy provision strategies. Ninety-six Hu sheep (body weight: 17.78 ± 1.24 kg) were equally assigned to four energy provision strategies: (1) low-energy diet for the whole finishing stage (LL); (2) high-energy diet for the whole finishing stage (HH); (3) low-energy diet in the early finishing stage and high-energy diet in the late finishing stage (LH); (4) high-energy diet in the early finishing stage and low-energy diet in the late finishing stage (HL). The results showed that the proportion of acetate was lower in the HH group than that in the HL group, whereas the opposite result was observed for the butyrate proportion (p < 0.05). The Chao 1, observed species, PD whole tree, and Shannon index of the rumen bacteria were higher in the LL group than that in the HH group (p < 0.05). The taxonomic annotations revealed that the Patescibacteria, Rikenellaceae RC9 gut group, Christensenellaceae R-7 group, and Anaeroplasma abundances were higher in the HL group than that in the HH group, and the opposite results were observed regarding the relative abundances of Selenomonas and Anaerovibrio (p < 0.05). The relative abundances of Spirochaetota and Treponema were higher in the LH group than that in the HH group (p < 0.05). Moreover, the analysis of similarity (ANOSIM) showed significant differences between groups (R = 0.6792 and p = 0.001). This study indicates that the energy provision strategy had little impact on the rumen fermentation characteristics, while it heavily affected the rumen bacterial diversity and community composition. This study may provide insight into the rumen fermentation characteristics and bacterial community under routine finishing models and contribute to the optimization of energy provision strategies of Hu sheep.

Effects of sponge iron dosage on nitrogen removal performance and microbial community structure in sequencing batch reactors

The application of sponge iron (SI) carriers can improve the biochemical treatment performance of sequencing batch reactors (SBR) during wastewater treatment. This study used SBR reactors to explore the effects of SI dosage on the nitrogen removal performance and reactor stability and microbial community structure under low temperature and ultra-low load. In contrast to conventional SBR, the average removal rate of total nitrogen (TN) in the biological sponge iron system (BSIS) was increased by 5.38 % for 45 g/L, 18.93 % for 90 g/L, and 13.52 % for 135 g/L, respectively. The nitrogen removal performance and reactor stability showed the best performance under the SI dosage of 90 g/L. The addition of SI formed the anaerobic-anoxic-aerobic microenvironments, which facilitate the propagation of denitrifying bacteria (Saccharimonadales, Hydrogenophaga) and iron bacteria (Rhodoferax and Acinetobacter) in the BSIS. This study provides a new insight on the application of SI in the wastewater treatment.

From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors

Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.

Occurrence, Diversity, and Genomes of "Candidatus Patescibacteria" along the Early Diagenesis of Marine Sediments

The phylum "Candidatus Patescibacteria" (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain "Ca. Patescibacteria" (0.4 to 28% of the total communities), which are affiliated with the classes "Ca. Paceibacteria," "Ca. Gracilibacteria," "Ca. Microgenomatia," "Ca. Saccharimonadia," "Ca. ABY1," and "Ca. WWE3." However, only a subset of the diversity of marine sediment "Ca. Patescibacteria," especially the classes "Ca. Paceibacteria" and "Ca. Gracilibacteria," can be captured by 16S rRNA gene amplicon sequencing with commonly used universal primers. We recovered 11 metagenome-assembled genomes (MAGs) of CPR from these sediments, most of which are novel at the family or genus level in the "Ca. Paceibacteria" class and are missed by the amplicon sequencing. While individual MAGs are confined to specific anoxic niches, the lack of capacities to utilize the prevailing terminal electron acceptors indicates that they may not be directly selected by the local redox conditions. These CPR bacteria lack essential biosynthesis pathways and may use a truncated glycolysis pathway to conserve energy as fermentative organotrophs. Our findings suggest that marine sediments harbor some novel yet widespread CPR bacteria during the early diagenesis of organic matter, which needs to be considered in population dynamics assessments in this vast environment. IMPORTANCE Ultrasmall-celled "Ca. Patescibacteria" have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized. By applying cultivation-independent approaches to a range of sediment redox zones, we reveal that "Ca. Patescibacteria" members are rare but widespread regardless of the prevailing geochemical conditions. These bacteria are affiliated with novel branches of "Ca. Patescibacteria" and have been largely missed in marker gene-based surveys. They do not have respiration capacity but may conserve energy by fermenting organic compounds from their episymbiotic hosts. Our findings suggest that these novel "Ca. Patescibacteria" are among the previously overlooked microbes in diverse marine sediments.

Geogenic arsenic and arsenotrophic microbiome in groundwater from the Hetao Basin

High arsenic (As) in groundwater is an environmental issue of global concern, which is closely related to microbe-mediated As biogeochemical cycling. However, the distribution of genes related to As cycling and underlying microbial As biogeochemical processes in high As groundwater remain elusive. Hence, we profiled the As cycling genes (arsC, arrA, and aioA genes) and indigenous microbial communities in groundwater from a typical high As area, the Hetao Basin from China, using amplicon sequencing and qPCR techniques. Here, we revealed the significant difference in microbial community structure between low As groundwater samples (LG) and high As groundwater samples (HG). Acinetobacter, Thiovirga, Hydrogenophaga, and Sulfurimonas were dominant in LG, while Aquabcterium, Acinetobacter, Sphingomonas, Pseudomonas, Desulfomicrobium, Hydrogenophaga, and Nitrospira were predominant in HG. Shannon and Chao indices of the microbial communities in HG were significantly higher than those of in LG. Alpha diversity and abundance of arsC and arrA genes were higher than those of aioA genes. The significant positive correlation was uncovered between the abundances of arsC and aioA genes, suggesting the cooccurrence of As functional genes in groundwater. Sphingopyxis, Agrobacterium, Klebsiella, Hoeflea, and Aeromonas represented the dominant taxa within the As (V) reducers communities. Distance-based redundancy analysis showed that ORP, pH, As_tot, Mn, and DOC were the key factors shaping the diverse microbial populations, while ORP, S^2-, As(III), Fe(II), NH₄⁺, pH, Mn, SO₄^2-, As(V), temperature, and P as the main drivers affecting arsenotrophic microbiota. This work provides an insight into microbial communities linked to As biogeochemical processes in high As groundwater, playing a fundamental role in groundwater As cycling.

Microbial assembly and co-occurrence network in an aquifer under press perturbation

Purpose

Thousands of aquifers worldwide have been polluted by leachate from landfills and many more remained threatened. Microbial communities from these environments play a crucial role in mediating biodegradation and maintaining the biogeochemical cycles, but their co-occurrence and assembly mechanism have not been investigated.

Method

Here, we coupled network analysis with multivariate statistics to assess the relative importance of deterministic versus stochastic microbial assembly in an aquifer undergoing intrinsic remediation, using 16S metabarcoding data generated through Illumina MiSeq sequencing of the archaeal/bacterial V3–V4 hypervariable region.

Results

Results show that both the aquifer-wide and localised community co-occurrences deviate from expectations under null models, indicating the predominance of deterministic processes in shaping the microbial communities. Further, the amount of variation in the microbial community explained by the measured environmental variables was 55.3%, which illustrates the importance of causal factors in forming the structure of microbial communities in the aquifer. Based on the network topology, several putative keystone taxa were identified which varied remarkably among the wells in terms of their number and composition. They included Nitrospira, Nitrosomonadaceae, Patulibacter, Legionella, uncharacterised Chloroflexi, Vicinamibacteriales, Neisseriaceae, Gemmatimonadaceae, and Steroidobacteraceae. The putative keystone taxa may be providing crucial functions in the aquifer ranging from nitrogen cycling by Nitrospira, Nitrosomonadaceae, and Steroidobacteraceae, to phosphorous bioaccumulation by Gemmatimonadaceae.

Conclusion

Collectively, the findings provide answers to fundamental ecological questions which improve our understanding of the microbial ecology of landfill leachate plumes, an ecosystem that remains understudied.

Enhancement of nutrients removal and biomass accumulation of algal-bacterial symbiosis system by optimizing the concentration and type of carbon source in the treatment of swine digestion effluent

The algae-bacteria symbiosis system (ABS) is used to effectively solve the problems of low carbon/nitrogen (C/N) ratio, low biodegradability and high ammonia toxicity in swine digestion effluent. This study examined the effects of the concentration and type of carbon source on ABS in the pollutants removal especially ammonia. When C/N ratio was 30:1 and carbon source was sodium acetate, the ABS was most conducive to the removal of nitrogen, phosphorus and COD, and to the accumulation of biomass and lipids. To make the wastewater discharge meet the relevant standard, the ABS + mono-cultivation of algae reprocessing system (MAS), was applied to actual swine digestion effluent. Through adjusting the C/N ratio in ABS to 30:1, the biomass concentration was 2.06 times higher than that of raw wastewater, and the removal efficiencies of NH₄⁺-N, TN, TP and COD increased by 1.43, 1.46, 1.95 and 1.28 times, respectively. The final concentrations of NH₄⁺-N, TN, TP and COD after the treatment of ABS (C/N ratio of 30:1) + MAS, were 16.98 ± 1.07 mg L^-1, 18.72 ± 1.81 mg L^-1, 0.48 ± 0.01 mg L^-1 and 263.49 ± 11.89 mg L^-1, respectively, reached the Chinese discharge standards for livestock and poultry wastewater. Bacterial community analysis showed that the dominant species of the ABS (C/N ratio of 30:1) was Corynebacterium (genus level). This study revealed that adjusting the concentration and type of carbon source was helpful to the nutrient cycling and resource utilization of ABS, indicating a feasible technique for treating high ammonia nitrogen digestate.

Development of microbial communities in biofilm and activated sludge in a hybrid reactor

Microorganisms play a key role in biological wastewater treatment. The form in which biomass develops determines the efficiency and mechanisms of organic compound conversion, due to different conditions in various microbial structures. However, the results of studies comparing the microbial communities in biofilm and activated sludge have often conflicted. Therefore, this study compared the composition and development of the bacterial communities in biofilm and activated sludge in a hybrid reactor, employing 16S rRNA sequencing. Statistical analysis of the sequencing data included the identification of taxa characteristic to the biofilm and activated sludge, alpha and beta diversity analysis, and network analysis. These analyses indicated that the biofilm bacterial community was richer and more diverse than the activated sludge community. The mean numbers of OTU were 1614 in the biofilm and 993 in the activated sludge, and the mean values of the Chao1 (1735 vs. 1105) and Shannon (5.3 vs. 4.3) biodiversity indices were significantly higher for the biofilm. The biofilm was a better environment for development of nitrifiers (e.g., Nitrosomonas, Nitrospira) and phosphorus accumulating organisms (Candidatus Accumulibacter). Bacteria in the biofilm co-occurrence network had more connections (based on Spearman's rank correlation coefficient) with each other, indicating that they interact more than those in the activated sludge.

Exploration of pristine plate-tectonic plains and mining exposure areas for indigenous microbial communities and its impact on the mineral-microbial geochemical weathering process in ultramafic setting

Heavy metal release from harsh ultramafic settings influences microbial diversity and function in soil ecology. This study aimed to determine how serpentine mineralosphere bacterial assemblies and their functions differed in two different plate-tectonic plains and mining exposure sites under heavy metal release conditions. The results showed that the Proteobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Chloroflexi were the most abundant bacterial groups among all the sites. The log10-based LDA scores highlighted that some specific groups of bacterial assemblies were enriched in plate-tectonic plains and mining activity areas of the serpentine mineralosphere. Functional prediction revealed that the abundance of heavy metal (Cr and Ni) resistance and biogeochemical cycles involving functional KEGG orthology varied in samples from plate-tectonic plains and mining activity sites. The bipartite plot showed that the enrichment of the biogeochemical cycle and heavy metal resistance functional genes correlated with the abundance of serpentine mineralosphere bacterial groups at a 0.005% confidence level. The co-occurrence network plot revealed that the interconnection pattern of the indigenous bacterial assemblies changed in different plate-tectonic plains and mining exposure areas. Finally, this study concluded that due to heavy metal release, the variation in bacterial assemblies, their functioning, and intercommunity co-occurrence patterns were clarified the synergetic effect of mineral-microbial geochemical weathering process in serpentine mining areas.

High spatial heterogeneity and low connectivity of bacterial communities along a Mediterranean subterranean estuary

Subterranean estuaries are biogeochemically active coastal sites resulting from the underground mixing of fresh aquifer groundwater and seawater. In these systems, microbial activity can largely transform the chemical elements that may reach the sea through submarine groundwater discharge (SGD), but little is known about the microorganisms thriving in these land-sea transition zones. We present the first spatially-resolved characterization of the bacterial assemblages along a coastal aquifer in the NW Mediterranean, considering the entire subsurface salinity gradient. Combining bulk heterotrophic activity measurements, flow cytometry, microscopy and 16S rRNA gene sequencing we find large variations in prokaryotic abundances, cell size, activity and diversity at both the horizontal and vertical scales that reflect the pronounced physicochemical gradients. The parts of the transect most influenced by freshwater were characterized by smaller cells and lower prokaryotic abundances and heterotrophic production, but some activity hotspots were found at deep low-oxygen saline groundwater sites enriched in nitrite and ammonium. Diverse, heterogeneous and highly endemic communities dominated by Proteobacteria, Patescibacteria, Desulfobacterota and Bacteroidota were observed throughout the aquifer, pointing to clearly differentiated prokaryotic niches across these transition zones and little microbial connectivity between groundwater and Mediterranean seawater habitats. Finally, experimental manipulations unveiled large increases in community heterotrophic activity driven by fast growth of some rare and site-specific groundwater Proteobacteria. Our results indicate that prokaryotic communities within subterranean estuaries are highly heterogeneous in terms of biomass, activity and diversity, suggesting that their role in transforming nutrients will also vary spatially within these terrestrial-marine transition zones.

Microbial diversity and geochemistry of groundwater impacted by steel slag leachates

To understand long-term impacts of steel slag material on aquifer geochemistry and microbial communities, we conducted four sampling campaigns in the Gier alluvial groundwater (Loire, France). In its northern part, the aquifer flows under a 200,000 m³ steel slag exhibiting high levels of chromium and molybdenum. Geochemical analyses of the water table revealed the existence of water masses with different chemical signatures. They allowed us to identify an area particularly contaminated by leachates from the slag heap, whatever the sampling period. Water samples from this area were compared to non-contaminated samples, with geochemical characteristics similar to the river samples. To follow changes in microbial communities, the V3-V4 region of 16 s rRNA gene was sequenced. Overall, we observed lower diversity indices in contaminated areas, with higher relative abundances of Verrucomicrobiota and Myxococcota phyla, while several Proteobacteria orders exhibited lower relative abundances. In particular, one single genus among the Verrucomicrobiota, Candidatus Omnitrophus, represented up to 36 % of total taxon abundance in areas affected by steel slag leachates. A large proportion of taxa identified in groundwater were also detected in the upstream river, indicating strong river-groundwater interactions. Our findings pave the way for future research work on C. Omnitrophus remediation capacities.

Research of cervical microbiota alterations with human papillomavirus infection status and women age in Sanmenxia area of China

Background

Human papillomavirus (HPV) infection is the leading cause of cervical cancer. More and more studies discovered that cervical microbiota (CM) composition correlated with HPV infection and the development of cervical cancer. However, more studies need to be implemented to clarify the complex interaction between microbiota and the mechanism of disease development, especially in a specific area of China.

Materials and methods

In this study, 16S rDNA sequencing was applied on 276 Thin-prep Cytologic Test (TCT) samples of patients from the Sanmenxia area. Systematical analysis of the microbiota structure, diversity, group, and functional differences between different HPV infection groups and age groups, and co-occurrence relationships of the microbiota was carried out.

Results

The major microbiota compositions of all patients include Lactobacillus iners, Escherichia coli, Enterococcus faecalis, and Atopobium vaginae at species level, and Staphylococcus, Lactobacillus, Gardnerella, Bosea, Streptococcus, and Sneathia in genus level. Microbiota diversity was found significantly different between HPV-positive (Chao1 index: 98.8869, p < 0.01), unique-268 infected (infections with one of the HPV genotype 52, 56, or 58, 107.3885, p < 0.01), multi-268 infected (infections with two or more of HPV genotype 52, 56, and 58, 97.5337, p = 0.1012), other1 (94.9619, p < 0.05) groups and HPV-negative group (83.5299). Women older than 60 years old have higher microbiota diversity (108.8851, p < 0.01, n = 255) than younger women (87.0171, n = 21). The abundance of Gardnerella and Atopobium vaginae was significantly higher in the HPV-positive group than in the HPV-negative group, while Burkholderiaceae and Mycoplasma were more abundant in the unique-268 group compared to the negative group. Gamma-proteobacteria and Pseudomonas were found more abundant in older than 60 patients than younger groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) analysis revealed the effects on metabolism by microbiota that the metabolism of cells, proteins, and genetic information-related pathways significantly differed between HPV-negative and positive groups. In contrast, lipid metabolism, signal transduction, and cell cycle metabolism pathway significantly differed between multi-268 and negative groups.

Conclusion

The HPV infection status and age of women were related to CM’s diversity and function pathways. The complex CM co-occurrent relationships and their mechanism in disease development need to be further investigated.

Microbial Response to Increased Temperatures Within a Lava-Induced Hydrothermal System in Iceland: An Analogue for the Habitability of Volcanic Terrains on Mars

Fossil hydrothermal systems on Mars are important exploration targets because they may have once been habitable and could still preserve evidence of microbial life. We investigated microbial communities within an active lava-induced hydrothermal system associated with the 2014-2015 eruption of Holuhraun in Iceland as a Mars analogue. In 2016, the microbial composition in the lava-heated water differed substantially from that of the glacial river and spring water sources that fed into the system. Several taxonomic and metabolic groups were confined to the water emerging from the lava and some showed the highest sequence similarities to subsurface ecosystems, including to the predicted thermophilic and deeply branching Candidatus Acetothermum autotrophicum. Measurements show that the communities were affected by temperature and other environmental factors. In particular, comparing glacial river water incubated in situ (5.7°C, control) with glacial water incubated within a lava-heated stream (17.5°C, warm) showed that microbial abundance, richness, and diversity increased in the warm treatment compared with the control, with the predicted major metabolism shifting from lithotrophy toward organotrophy and possibly phototrophy. In addition, thermophilic bacteria isolated from the lava-heated water and a nearby acidic hydrothermal system included the known endospore-formers Geobacillus stearothermophilus and Paenibacillus cisolokensis as well as a potentially novel taxon within the order Hyphomicrobiales. Similar lava-water interactions on Mars could therefore have generated habitable environments for microbial communities.

Effects of different rotation cropping systems on potato yield, rhizosphere microbial community and soil biochemical properties

Continuous potato cropping systems cause yield reduction, soil-borne disease aggravation, and soil degradation, but crop rotation can alleviate these negative effects. However, there are limited studies on the relationships between microbial community and other soil biochemical properties of continuous potato cropping at both pre-planting and harvest in North China. A 4-year study was conducted to explore the effects of different rotation system on soil biochemical properties, microbial community at pre-planting and harvest, and potato yield, tuber number and black scurf incidence at harvest in 2020 and 2021, which included 4 treatments vis. potato-potato-potato-potato (PC), potato-oat-faba bean-potato (PR), oat-faba bean-potato-oat (O), and faba bean-potato-oat-faba bean (B). The results showed that soil biochemical properties and microbial community among all treatments showed no significant difference at pre-planting after a long cold winter generally. At harvest, PC reduced tuber yield and number and significantly increased black scurf incidence relative to potato rotation systems. PC also reduced soil enzyme activities, the content of soil nutrients, and fungal community diversity, and increased bacterial community diversity compared with the other treatments, insignificantly when compared with PR. Relative abundance of microorganisms related to the degradation of organic residues, soil nitrogen cycling, and disease suppression, such as the genera Devosia, Aeromicrobium, Paraphoma, and Papiliotrema, were significantly higher in O or B than in PC and PR, while microorganisms related to disease infection such as the genera Pseudomonas, Colletotrichum, Plectosphaerella, Fusarium, and Verticillium exhibited increased in PC and PR. Principal Coordinates Analysis (PCoA) showed that there were significant differences in the microbial community structure of PC and PR at harvest compared with that of O and B. Redundancy analysis (RDA) revealed that soil available potassium (AK), acid phosphatase (ACP), available phosphorus (AP), sucrase (SUC) and pH were the dominant factors that significantly affected bacterial and fungal community structure. Partial least squares structural equation model indicated rotation system had significant negative effect on fungal community. It was concluded that growing oat or faba bean after potato can increase soil beneficial microorganisms and maintain the ecosystem healthy, thus reducing the incidence of tuber black scurf and increasing potato yield.

Water Physicochemical Parameters and Microbial Composition Distinguish Anopheles and Culex Mosquito Breeding Sites: Potential as Ecological Markers for Larval Source Surveillance

The presence of mosquitoes in an area is dependent on the availability of suitable breeding sites that are influenced by several environmental factors. Identification of breeding habitats for vector surveillance and larval source management is key to disease control programs. We investigated water quality parameters and microbial composition in selected mosquito breeding sites in urban Accra, Ghana and associated these with abundance of Anopheles (Diptera: Culicidae) and Culex (Diptera: Culicidae) larvae. Physicochemical parameters and microbial composition explained up to 72% variance among the breeding sites and separated Anopheles and Culex habitats (P < 0.05). Anopheles and Culex abundances were commonly influenced by water temperature, pH, nitrate, and total hardness with contrasting impacts on the two mosquito species. In addition, total dissolved solids, biochemical oxygen demand, and alkalinity uniquely influenced Anopheles abundance, while total suspended solids, phosphate, sulphate, ammonium, and salinity were significant determinants for Culex. The correlation of these multiple parameters with the occurrence of each mosquito species was high (R2 = 0.99, P < 0.0001). Bacterial content assessment of the breeding ponds revealed that the most abundant bacterial phyla were Patescibacteria, Cyanobacteria, and Proteobacteria, constituting >70% of the total bacterial richness. The oligotrophic Patescibacteria was strongly associated with Anopheles suggestive of the mosquito's adaptation to environments with less nutrients, while predominance of Cyanobacteria, indicative of rich nutritional source was associated with Culex larval ponds. We propose further evaluation of these significant abiotic and biotic parameters in field identification of larval sources and how knowledge of these can be harnessed effectively to reduce conducive breeding sites for mosquitoes.

Multiomics analyses uncover nanoceria triggered oxidative injury and nutrient imbalance in earthworm Eisenia fetida

The toxic stress caused by nanoceria remains vague owing to the limited efforts scrutinizing its molecular mechanisms. Herein, we investigated the impacts of nanoceria on earthworm Eisenia fetida, at the molecular level using the multiomics-based profiling approaches (transcriptomics, metabolomics, and 16 S rRNA sequencing). Nanoceria (50 and 500 mg/kg) significantly increased the contents of malondialdehyde (MDA), Fe, and K in worms, suggesting oxidative injury and nutrient imbalance. This was corroborated by the transcriptomic and metabolomic analyses. Nanoceria decreased the levels of certain genes and metabolites associated with glycerolipid and glycerophospholipid metabolisms, suggesting the production of reactive oxygen species and subsequent oxidative stress. Additionally, the ABCD3 gene belonging to ABC transporter family was upregulated, facilitating Fe uptake by worms. Moreover, the higher contents of MDA, Fe, and K after exposure were tightly associated with the imbalanced intestinal flora. Specifically, a higher relative abundance of Actinobacteriota and a lower relative abundance of Proteobacteria and Patescibacteria were induced. This study, for the first time, revealed that nanoceria at nonlethal levels caused oxidative stress and nutrient imbalance of earthworms from the perspective of genes, metabolites, and gut microbiome perturbations, and also established links between the gut microbiome and the overall physiological responses of the host.

Exogenous Melatonin Reprograms the Rhizosphere Microbial Community to Modulate the Responses of Barley to Drought Stress

The rhizospheric melatonin application-induced drought tolerance has been illuminated in various plant species, while the roles of the rhizosphere microbial community in this process are still unclear. Here, the diversity and functions of the rhizosphere microbial community and related physiological parameters were tested in barley under the rhizospheric melatonin application and drought. Exogenous melatonin improved plant performance under drought via increasing the activities of non-structural carbohydrate metabolism enzymes and activating the antioxidant enzyme systems in barley roots under drought. The 16S/ITS rRNA gene sequencing revealed that drought and melatonin altered the compositions of the microbiome. Exogenous melatonin increased the relative abundance of the bacterial community in carbohydrate and carboxylate degradation, while decreasing the relative abundance in the pathways of fatty acid and lipid degradation and inorganic nutrient metabolism under drought. These results suggest that the effects of melatonin on rhizosphere microbes and nutrient condition need to be considered in its application for crop drought-resistant cultivation.

One-step PCR amplicon sequencing libraries perform better than two-step when assessing soil microbial diversity and community profiles

Despite adoption of high-throughput sequencing of PCR-amplified microbial taxonomic markers for ecological analyses, distinct approaches for preparing amplicon libraries exist. One approach utilises long fusion primers and a single PCR (one-step) while another utilises shorter primers in a first reaction, before transferring diluted amplicons to a second reaction for barcode index incorporation (two-step). We investigated whether transferring diluted amplicons risked creating artificially simplified, poorly diverse communities. In soils from three sites with paired cropland and forest, one-step yielded higher alpha-diversity indices, including detection of two-four times more unique taxa. Modelling expected taxa per sequence observation predicted that one-step reaches full coverage by 104 sequences per sample while two-step needs 105-109. Comparisons of rank abundance demonstrated that two-step covered only 38-69% of distributions. Beta-diversity showed better separation of communities in response to land use change under one-step, although both approaches showed a significant effect. Driving differences was underestimation of relatively minor taxa with the two-step procedure. These taxa were low in abundance, yet play important roles in carbon cycling, secondary metabolite production, anaerobic metabolism, and bacterial predation. We conclude that one-step amplicon libraries are advisable for studies focussed on diversity or relatively minor yet functionally important taxa.

Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield

The deep terrestrial biosphere encompasses the life below the photosynthesis-fueled surface that perseveres in typically nutrient and energy depleted anoxic groundwaters. The composition and cycling of this vast dissolved organic matter (DOM) reservoir relevant to the global carbon cycle remains to be deciphered. Here we show that recent Baltic Sea-influenced to ancient pre-Holocene saline Fennoscandian Shield deep bedrock fracture waters carried DOM with a strong terrigenous signature and varying contributions from abiotic and biotic processes. Removal of easily degraded carbon at the surface-to-groundwater transition and corresponding microbial community assembly processes likely resulted in the highly similar DOM signatures across the notably different water types that selected for a core microbiome. In combination with the aliphatic character, depleted δ¹³C signatures in DOM indicated recent microbial production in the oldest, saline groundwater. Our study revealed the persistence of terrestrially-sourced carbon in severely energy limited deep continental groundwaters supporting deep microbial life.