Acidobacteria Subgroups and Their Metabolic Potential for Carbon Degradation in Sugarcane Soil Amended With Vinasse and Nitrogen Fertilizers

Macrophage MAPK7/AhR/STAT3 Signaling Mediates Mitochondrial ROS Burst and Enterohepatic Inflammatory Responses Induced by Deoxynivalenol Relevant to Low-Dose Exposure in Children

Deoxynivalenol (DON) can induce endoplasmic reticulum (ER) stress, mitochondrial ROS burst, and macrophage polarization. Here, we investigated the mechanism linking the above three aspects with the dose range relevant to low-level exposure in children. At 0.5 μg/kg bw/day, we found remarkable liver and gut inflammatory responses after 6-week exposure in mice age comparable to humans 7-12 years old. Through antioxidant intervention, we found that ROS played a driver role in macrophage polarization and inflammatory responses induced by DON in the liver and gut. Further bioinformatics analysis uncovered that ER stress-associated protein MAPK7 (ERK5) may bind with AhR to initiate a mitochondrial ROS burst and macrophage M1 polarization. The downstream cellular events of MAPK7-AhR interaction may be mediated by the AhR/STAT3/p-STAT(Ser727) pathway. This mechanism was further supported by DON toxicity mitigation using cyanidin-3-glucoside (C-3-G), which docks to MAPK7 oligomerization region 200-400 aa and disrupts MAPK7-AhR interaction. Overall, our study provides novel evidence and mechanism for DON-induced inflammatory responses in the liver and gut system. Our findings call attention to the health risks associated with low-level DON exposure in the prepuberty children population.

Perfluorooctanoic acid effect and microbial mechanism to methane production in anaerobic digestion

Perfluorooctanoic acid (PFOA) as emerging pollutants was largely produced and stable in nature environment. Its fate and effect to the wasted sludge digestion process and corresponding microbial mechanism was rarely reported. This study investigated the different dose of PFOA to the wasted sludge digestion process, where the methane yield and microbial mechanism was illustrated. The PFOA added before digestion were 0-10000 μg/L, no significant variation in daily and accumulated methane production between each group. The 9th day methane yield was significantly higher than other days (p < 0.05). The soluble protein was significantly decreased after 76 days digestion (p < 0.001). The total PFOA in sludge (R2 = 0.8817) and liquid (R2 = 0.9083) phase after digestion was exponentially correlated with PFOA dosed. The PFOA in liquid phase was occupied 54.10 ± 18.38% of the total PFOA in all reactors. The dewatering rate was keep decreasing with the increase of PFOA added (R2 = 0.7748, p < 0.001). The mcrA abundance was significantly correlated with the pH value and organic matter concentration in the reactors. Chloroflexi was the predominant phyla, Aminicenantales, Bellilinea and Candidatus_Cloacimonas were predominant genera in all reactors. Candidatus_Methanofastidiosum and Methanolinea were predominant archaea in all reactors. The function prediction by FAPROTAX and Tax4fun implied that various PFOA dosage resulted in significant function variation. The fermentation and anaerobic chemoheterotrophy function were improved with the PFOA dose. Co-occurrence network implied the potent cooperation among the organic matter degradation and methanogenic microbe in the digestion system. PFOA has little impact to the methane generation while affect the microbe function significantly, its remaining in the digested sludge should be concerned to reduce its potential environmental risks.

Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea

Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.

Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter

Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we 13CO2-labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar 13C enrichment. SOM density fractionation, 13C NMR, and IRMS showed AMF transferred 0.77 mg C g-1 of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported 13C (> 20 atom%). Mapping sequences from 13C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly 13C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.

Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA

Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ34SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.

Microbiological exploration of the Cueva del Viento lava tube system in Tenerife, Canary Islands

Cueva del Viento, located in the Canary Islands, Spain, is the Earth's sixth-longest lava tube, spanning 18,500 m, and was formed approximately 27,000 years ago. This complex volcanic cave system is characterized by a unique geomorphology, featuring an intricate network of galleries. Despite its geological significance, the geomicrobiology of Cueva del Viento remains largely unexplored. This study employed a combination of culture-dependent techniques and metabarcoding data analysis to gain a comprehensive understanding of the cave's microbial diversity. The 16S rRNA gene metabarcoding approach revealed that the coloured microbial mats (yellow, red and white) coating the cave walls are dominated by the phyla Actinomycetota, Pseudomonadota and Acidobacteriota. Of particular interest is the high relative abundance of the genus Crossiella, which is involved in urease-mediated biomineralization processes, along with the presence of genera associated with nitrogen cycling, such as Nitrospira. Culture-dependent techniques provided insights into the morphological characteristics of the isolated species and their potential metabolic activities, particularly for the strains Streptomyces spp., Paenarthrobacter sp. and Pseudomonas spp. Our findings underscore the potential of Cueva del Viento as an ideal environment for studying microbial diversity and for the isolation and characterization of novel bacterial species of biotechnological interest.

Effects of running time on biological activated carbon filters: water purification performance and microbial community evolution

Ozone-biologically activated carbon (BAC) filtration is an advanced treatment process that can be applied to remove recalcitrant organic micro-pollutants in drinking water treatment plants (DWTPs). In this study, we continuously monitored a new and an old BAC filter in a DWTP for 1 year to compare their water purification performance and microbial community evolution. The results revealed that, compared with the new filter, the use of the old BAC filter facilitated a slightly lower rate of dissolved organic carbon (DOC) removal. In the case of the new BAC filter, we recorded general increases in the biomass and microbial diversity of the biofilm with a prolongation of operating time, with the biomass stabilizing after 7 months. For both new and old BAC filters, Proteobacteria and Acidobacteria were the dominant bacterial phyla. At the genus level, the microbial community gradually shifted over the course of operation from a predominance of Herminiimonas and Hydrogenophaga to one predominated by Bradyrhizbium, Bryobacter, Hyphomicrobium, and Pedomicrobium, with Bradyrhizobium being established as the most abundant genus in the old BAC filter. Regarding spatial distribution, we detected reductions in the biomass and number of operational taxonomic units with increasing biofilm depth, whereas there was a corresponding increase in microbial diversity. However, compared with the effects of time, the influence of depth on the composition of the biofilm microbial community was considerably smaller. Furthermore, co-occurrence network analysis revealed that the microbial community network of the new filter after 11 months of operation was the most tightly connected, although its modular coefficient was the lowest of those assessed. We speculate that the positive and negative interactions within the network may be attributable to symbiotic or competitive relationships among species. Moreover, there may have been a significant negative interaction between SWB02 and Acidovorax, plausibly associated with a competition for substrates.

Nutrient-dependent cross-kingdom interactions in the hyphosphere of an arbuscular mycorrhizal fungus

Introduction

The hyphosphere of arbuscular mycorrhizal (AM) fungi is teeming with microbial life. Yet, the influence of nutrient availability or nutrient forms on the hyphosphere microbiomes is still poorly understood.

Methods

Here, we examined how the microbial community (prokaryotic, fungal, protistan) was affected by the presence of the AM fungus Rhizophagus irregularis in the rhizosphere and the root-free zone, and how different nitrogen (N) and phosphorus (P) supplements into the root-free compartment influenced the communities.

Results

The presence of AM fungus greatly affected microbial communities both in the rhizosphere and the root-free zone, with prokaryotic communities being affected the most. Protists were the only group of microbes whose richness and diversity were significantly reduced by the presence of the AM fungus. Our results showed that the type of nutrients AM fungi encounter in localized patches modulate the structure of hyphosphere microbial communities. In contrast we did not observe any effects of the AM fungus on (non-mycorrhizal) fungal community composition. Compared to the non-mycorrhizal control, the root-free zone with the AM fungus (i.e., the AM fungal hyphosphere) was enriched with Alphaproteobacteria, some micropredatory and copiotroph bacterial taxa (e.g., Xanthomonadaceae and Bacteroidota), and the poorly characterized and not yet cultured Acidobacteriota subgroup GP17, especially when phytate was added. Ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira were significantly suppressed in the presence of the AM fungus in the root-free compartment, especially upon addition of inorganic N. Co-occurrence network analyses revealed that microbial communities in the root-free compartment were complex and interconnected with more keystone species when AM fungus was present, especially when the root-free compartment was amended with phytate.

Conclusion

Our study showed that the form of nutrients is an important driver of prokaryotic and eukaryotic community assembly in the AM fungal hyphosphere, despite the assumed presence of a stable and specific AM fungal hyphoplane microbiome. Predictable responses of specific microbial taxa will open the possibility of using them as co-inoculants with AM fungi, e.g., to improve crop performance.

16S metabarcoding analysis reveals the influence of organic and conventional farming practices on bacterial communities from the rhizospheric of Coffea arabica L

Coffea sp. is cultivated in many tropical countries. Brazil has always adopted intensive agricultural practices, but organic coffee farming is an alternative system based on the non-use of agrochemicals and the rational management of soils. Metabarcoding 16S analysis using next-generation sequencing has been developed to identify and compare the diversity of the Coffea arabica L. rhizospheric bacterial community in two farming areas in São Paulo, Brazil. Dourado uses conventional farming, while Ribeirão Corrente uses organic. We found broad taxonomic composition, with sequences from 24 phyla, 55 classes, 61 orders, 146 families, and 337genus. The three most abundant phyla were Proteobacteria (38.27%), Actinobacteria (15.56%), and Acidobacteria (16.10%). In organic farming, the top 3 were the family Sphingomonadaceae, order Rhizobiales, genus Nocardioides, and Gp6. The genus Gp2 and the phylum Candidatus Saccharibacteria were the most abundant OTUs exclusively present in conventional farming. In the organic farming practice, Proteobacteria, Actinobacteria, and Acidobacteria were also present among the exclusive OTUs; we also found OTUs belonging to Bacteroidetes, Firmicutes, and Verrucomicrobia. Our study indicates a positive effect of organic farming on microbial communities. Fertilization may directly affect soil microbiota, suggesting that a large and active microbial community low in functional diversity might not adapt to new climatic conditions. A diverse community could provide better resilience to environmental changes, improving the productivity of this important crop.

Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia

Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.

Acidobacteria members harbour an abundant and diverse carbohydrate-active enzymes (cazyme) and secreted proteasome repertoire, key factors for potential efficient biomass degradation

The Acidobacteria phylum is a very abundant group (20-30% of microbial communities in soil ecosystems); however, little is known about these microorganisms and their ability to degrade the biomass and lignocellulose due to the difficulty of culturing them. We, therefore, bioinformatically studied the content of lignocellulolytic enzymes (total and predicted secreted enzymes) and secreted peptidases in an in silico library containing 41 Acidobacteria genomes. The results showed a high abundance and diversity of total and secreted Carbohydrate-Active enzymes (cazyme) families among the Acidobacteria compared to known previous degraders. Indeed, the relative abundance of cazymes in some genomes represented more than 6% of the gene coding proteins with at least 300 cazymes. The same observation was made with the predicted secreted peptidases with several families of secreted peptidases, which represented at least 1.5% of the gene coding proteins in several genomes. These results allowed us to highlight the lignocellulolytic potential of the Acidobacteria phylum in the degradation of lignocellulosic biomass, which could explain its high abundance in the environment.

Archaea and their interactions with bacteria in a karst ecosystem

Karst ecosystems are widely distributed around the world, accounting for 15-20% of the global land area. However, knowledge on microbial ecology of these systems does not match with their global importance. To close this knowledge gap, we sampled three niches including weathered rock, sediment, and drip water inside the Heshang Cave and three types of soils overlying the cave (forest soil, farmland soil, and pristine karst soil). All these samples were subjected to high-throughput sequencing of V4-V5 region of 16S rRNA gene and analyzed with multivariate statistical analysis. Overall, archaeal communities were dominated by Thaumarchaeota, whereas Actinobacteria dominated bacterial communities. Thermoplasmata, Nitrosopumilaceae, Aenigmarchaeales, Crossiella, Acidothermus, and Solirubrobacter were the important predictor groups inside the Heshang Cave, which were correlated to NH4 + availability. In contrast, Candidatus Nitrososphaera, Candidatus Nitrocosmicus, Thaumarchaeota Group 1.1c, and Pseudonocardiaceae were the predictors outside the cave, whose distribution was correlated with pH, Ca2+, and NO2 -. Tighter network structures were found in archaeal communities than those of bacteria, whereas the topological properties of bacterial networks were more similar to those of total prokaryotic networks. Both chemolithoautotrophic archaea (Candidatus Methanoperedens and Nitrosopumilaceae) and bacteria (subgroup 7 of Acidobacteria and Rokubacteriales) were the dominant keystone taxa within the co-occurrence networks, potentially playing fundamental roles in obtaining energy under oligotrophic conditions and thus maintaining the stability of the cave ecosystem. To be noted, all the keystone taxa of karst ecosystems were related to nitrogen cycling, which needs further investigation, particularly the role of archaea. The predicted ecological functions in karst soils mainly related to carbohydrate metabolism, biotin metabolism, and synthesis of fatty acid. Our results offer new insights into archaeal ecology, their potential functions, and archaeal interactions with bacteria, which enhance our understanding about the microbial dark matter in the subsurface karst ecosystems.

Long-term continuous mono-cropping of Macadamia integrifolia greatly affects soil physicochemical properties, rhizospheric bacterial diversity, and metabolite contents

Macadamia integrifolia is the most economically important Proteaceae crop known for its edible nuts. The present study was conducted to examine the effect of continuous cultivation (for 1, 5, and 20 years) of M. integrifolia on soil quality, bacterial diversity, and metabolites. Soil rhizospheres from three different Macadamia rhizosphere orchards, 1-year monoculture orchard (CK), 5-year monoculture orchard (Y5), and 20-year monoculture orchard (Y20), were analyzed through metagenomic and metabolomic profiling. The soil physicochemical properties, including organic matter, and available nutrients (P, N, and K) were first increased significantly (p &lt; 0.05) from the CK to the Y5 group and then decreased (p &lt; 0.05) from the Y5 to the Y20 group. The soil pH continuously decreased (p &lt; 0.05) over time from CK to Y20. Metagenomic profiling revealed that Actinobacteria, Acidobacteria, and Proteobacteria were the top three abundant phyla with their inconsistent relative abundance patterns from CK to Y20 (CK: 23.76%, Y5: 34. 06%, and Y20: 31.55%), (CK: 13.59%, Y5: 18.59%, and Y20: 21.35%), and (CK: 27.59%, Y5: 15.98%, and Y20: 17.08%), respectively. Furthermore, the Y5 rhizospheres had a higher number of beneficial bacterial genera belonging to Proteobacteria and Actinobacteria than the Y20 rhizospheres. The KEGG annotation analysis revealed that cellular processes, organism systems, metabolism, and genetic information were the most enriched functional categories. CAZy database screening indicated the highest enrichment of glycoside hydrolases following the glycoside transferases and carbohydrate-binding modules. Differential metabolite analysis revealed the highest number of metabolites (11) in the Y5 group than in the Y20 group (6). It is concluded that continuous monoculture of M. integrifolia improves the soil physicochemical properties, bacterial diversity, and metabolite contents in short-term planted orchards which, however, are deteriorated in long-term planted orchards.

A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ¹³C and δ¹⁵N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.

Functional and Seasonal Changes in the Structure of Microbiome Inhabiting Bottom Sediments of a Pond Intended for Ecological King Carp Farming

Simple Summary

Bottom sediments are usually classified as extreme habitats for microorganisms. They are defined as matter deposited on the bottom of water bodies through the sedimentation process. The quality of sediments is extremely important for the good environmental status of water, because they are an integral part of the surface water environment. Microorganisms living in sediments are involved in biogeochemical transformations and play a fundamental role in maintaining water purity, decomposition of organic matter, and primary production. As a rule, studies on bottom sediments focus on monitoring their chemistry and pollution, while little is known about the structure of bacterial communities inhabiting this extreme environment. In this study, Next-Generation Sequencing (NGS) was combined with the Community-Level Physiological Profiling (CLPP) technique to obtain a holistic picture of bacterial biodiversity in the bottom sediments from Cardinal Pond intended for ecological king carp farming. It was evident that the bottom sediments of the studied pond were characterized by a rich microbiota composition, whose structure and activity depended on the season, and the most extensive modifications of the biodiversity and functionality of microorganisms were noted in summer.

Abstract

The main goal of the study was to determine changes in the bacterial structure in bottom sediments occurring over the seasons of the year and to estimate microbial metabolic activity. Bottom sediments were collected four times in the year (spring, summer, autumn, and winter) from 10 different measurement points in Cardinal Pond (Ślesin, NW Poland). The Next-Generation Sequencing (MiSeq Illumina) and Community-Level Physiological Profiling techniques were used for identification of the bacterial diversity structure and bacterial metabolic and functional activities over the four seasons. It was evident that Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant phyla, while representatives of Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria predominated at the class level in the bottom sediments. An impact of the season on biodiversity and metabolic activity was revealed with the emphasis that the environmental conditions in summer modified the studied parameters most strongly. Carboxylic and acetic acids and carbohydrates were metabolized most frequently, whereas aerobic respiration I with the use of cytochrome C was the main pathway used by the microbiome of the studied bottom sediments.

Comparison of bacterial communities and their functional profiling using 16S rRNA gene sequencing between the inherent serpentine-associated sites, hyper-accumulator, downgradient agricultural farmlands, and distal non-serpentine soils

This study aims to determine and compare the bacterial community and functional profiles associated with serpentine sites, innate hyper-accumulating weed, downgradient agricultural farmlands and non-serpentine sites using 16S rRNA gene sequencing. Elemental analysis revealed that the serpentine rock and weathered soil have higher magnesium, nickel, chromium, magnesium/calcium and lower calcium/magnesium ratios and agricultural farmlands have recorded elevated chromium. Proteobacteria were found predominant, except the non-serpentine site which was rich in Cyanobacteria. PCA analysis at the genus level indicates the uniqueness of different experimental groups, except the hyperaccumulators which exhibited relatively less dissimilarity. The shift analysis showed the serpentine sites were characterized by the abundance of bacteria having heavy metal effluxion. The hyper-accumulating weeds were higher in plant growth-promoting bacteria expressing tolerance against heavy metals toxicity such as nickel, chromium, cobalt and arsenic. Besides, the agricultural lands were abundant in wetland-associated methanogens and metal (manganese, iron and zinc) transporting function related bacteria. The results suggest that the inherent edaphic factors including heavy metal content, the interacting behavior of hyperaccumulator's rhizosphere microbiota with soil and anthropogenic activities such as agricultural practices could be a major determinant of the variation in the bacterial community selection and abundance in the respective study sites.

Microbial mercury transformations: Molecules, functions and organisms

Mercury (Hg) methylation, methylmercury (MeHg) demethylation, and inorganic redox transformations of Hg are microbe-mediating processes that determine the fate and cycling of Hg and MeHg in many environments, and by doing so influence the health of humans and wild life. The discovery of the Hg methylation genes, hgcAB, in the last decade together with advances in high throughput and genome sequencing methods, have resulted in an expanded appreciation of the diversity of Hg methylating microbes. This review aims to describe experimentally confirmed and recently discovered hgcAB gene-carrying Hg methylating microbes; phylogenetic and taxonomic analyses are presented. In addition, the current knowledge on transformation mechanisms, the organisms that carry them out, and the impact of environmental parameters on Hg methylation, MeHg demethylation, and inorganic Hg reduction and oxidation is summarized. This knowledge provides a foundation for future action toward mitigating the impact of environmental Hg pollution.

Long-Term, Simultaneous Impact of Antimicrobials on the Efficiency of Anaerobic Digestion of Sewage Sludge and Changes in the Microbial Community

The aim of this study was to evaluate the influence of simultaneous, long-term exposure to increasing concentrations of three classes of antimicrobials (β-lactams, fluoroquinolones and nitroimidazoles) on: (1) the efficiency of anaerobic digestion of sewage sludge, (2) qualitative and quantitative changes in microbial consortia that participate in methane fermentation, and (3) fate of antibiotic resistance genes (ARGs). Long-term supplementation of sewage sludge with a combination of metronidazole, amoxicillin and ciprofloxacin applied at different doses did not induce significant changes in process parameters, including the concentrations of volatile fatty acids (VFAs), or the total abundance of ARGs. Exposure to antibiotics significantly decreased methane production and modified microbial composition. The sequencing analysis revealed that the abundance of OTUs characteristic of Archaea was not correlated with the biogas production efficiency. The study also demonstrated that the hydrogen-dependent pathway of methylotrophic methanogenesis could significantly contribute to the stability of anaerobic digestion in the presence of antimicrobials. The greatest changes in microbial biodiversity were noted in substrate samples exposed to the highest dose of the tested antibiotics, relative to control. The widespread use of antimicrobials increases antibiotic concentrations in sewage sludge, which may decrease the efficiency of anaerobic digestion, and contribute to the spread of antibiotic resistance (AR).

The Evolution of Ecological Diversity in Acidobacteria

Acidobacteria occur in a large variety of ecosystems worldwide and are particularly abundant and highly diverse in soils. In spite of their diversity, only few species have been characterized to date which makes Acidobacteria one of the most poorly understood phyla among the domain Bacteria. We used a culture-independent niche modeling approach to elucidate ecological adaptations and their evolution for 4,154 operational taxonomic units (OTUs) of Acidobacteria across 150 different, comprehensively characterized grassland soils in Germany. Using the relative abundances of their 16S rRNA gene transcripts, the responses of active OTUs along gradients of 41 environmental variables were modeled using hierarchical logistic regression (HOF), which allowed to determine values for optimum activity for each variable (niche optima). By linking 16S rRNA transcripts to the phylogeny of full 16S rRNA gene sequences, we could trace the evolution of the different ecological adaptations during the diversification of Acidobacteria. This approach revealed a pronounced ecological diversification even among acidobacterial sister clades. Although the evolution of habitat adaptation was mainly cladogenic, it was disrupted by recurrent events of convergent evolution that resulted in frequent habitat switching within individual clades. Our findings indicate that the high diversity of soil acidobacterial communities is largely sustained by differential habitat adaptation even at the level of closely related species. A comparison of niche optima of individual OTUs with the phenotypic properties of their cultivated representatives showed that our niche modeling approach (1) correctly predicts those physiological properties that have been determined for cultivated species of Acidobacteria but (2) also provides ample information on ecological adaptations that cannot be inferred from standard taxonomic descriptions of bacterial isolates. These novel information on specific adaptations of not-yet-cultivated Acidobacteria can therefore guide future cultivation trials and likely will increase their cultivation success.

Comparative Genomics Reveal the Animal-Associated Features of the Acanthopleuribacteraceae Bacteria, and Description of Sulfidibacter corallicola gen. nov., sp., nov

Members of the phylum Acidobacteria are ubiquitous in various environments. Soil acidobacteria have been reported to present a variety of strategies for their success in terrestrial environments. However, owing to lack of pure culture, information on animal-associated acidobacteria are limited, except for those obtained from 16S rRNA genes. To date, only two acidobacteria have been isolated from animals, namely strain M133^T obtained from coral Porites lutea and Acanthopleuribacter pedis KCTC 12899^T isolated from chiton. Genomics and physiological characteristics of strain M133^T and A. pedis KCTC 12899^T were compared with 19 other isolates (one strain from each genus) in the phylum Acidobacteria. The results revealed that strain M133^T represents a new species in a new genus in the family Acanthopleuribacteraceae. To date, these two Acanthopleuribacteraceae isolates have the largest genomes (10.85–11.79 Mb) in the phylum Acidobacteria. Horizontal gene transfer and gene duplication influenced the structure and plasticity of these large genomes. Dissimilatory nitrate reduction and abundant secondary metabolite biosynthetic gene clusters (including eicosapentaenoic acid de novo biosynthesis) are two distinct features of the Acanthopleuribacteraceae bacteria in the phylum Acidobacteria. The absence of glycoside hydrolases involved in plant polysaccharide degradation and presence of animal disease-related peptidases indicate that these bacteria have evolved to adapt to the animal hosts. In addition to low- and high-affinity respiratory oxygen reductases, enzymes for nitrate to nitrogen, and sulfhydrogenase were also detected in strain M133^T, suggesting the capacity and flexibility to grow in aerobic and anaerobic environments. This study highlighted the differences in genome structure, carbohydrate and protein utilization, respiration, and secondary metabolism between animal-associated acidobacteria and other acidobacteria, especially the soil acidobacteria, displaying flexibility and versatility of the animal-associated acidobacteria in environmental adaption.

Influence of environmental factors on the tropical peatlands diazotrophic communities from the Southern Brazilian Atlantic Rain Forest

The tropical peatlands of southern Brazil are essential for the maintenance of the Atlantic Rain Forest, one of the 25 hotspots of biodiversity in the world. Although diazotrophic microorganisms are essential for the maintenance of this nitrogen limited ecosystem, so far studies have focused only on microorganisms involved in the carbon cycle. In this work, peat samples were collected from three tropical peatland regions during dry and rainy seasons and their chemical and microbial characteristics were evaluated. Our results showed that the structure of the diazotrophic communities in the Brazilian tropical peatlands differs in the evaluated seasons. The abundance of the genus Bradyrhizobium showed to be affected by rainfall and peat pH. Despite the shifts of the nitrogen fixing population in the tropical peatland caused by seasonality it showed to be constantly dominated by α-Proteobacteria followed by Cyanobacteria. In addition, more than 50% of nifH gene sequences have not been classified, indicating the necessity for more studies in tropical peatland, since the reduction of N supply in the peatlands stimulates the recalcitrant organic matter decomposition performed by peatland microorganisms, influencing the C stock.

Dynamics of Soil Microbial Communities During Diazepam and Oxazepam Biodegradation in Soil Flooded by Water From a WWTP

The demand for energy and chemicals is constantly growing, leading to an increase of the amounts of contaminants discharged to the environment. Among these, pharmaceutical molecules are frequently found in treated wastewater that is discharged into superficial waters. Indeed, wastewater treatment plants (WWTPs) are designed to remove organic pollution from urban effluents but are not specific, especially toward contaminants of emerging concern (CECs), which finally reach the natural environment. In this context, it is important to study the fate of micropollutants, especially in a soil aquifer treatment (SAT) context for water from WWTPs, and for the most persistent molecules such as benzodiazepines. In the present study, soils sampled in a reed bed frequently flooded by water from a WWTP were spiked with diazepam and oxazepam in microcosms, and their concentrations were monitored for 97 days. It appeared that the two molecules were completely degraded after 15 days of incubation. Samples were collected during the experiment in order to follow the dynamics of the microbial communities, based on 16S rRNA gene sequencing for Archaea and Bacteria, and ITS2 gene for Fungi. The evolution of diversity and of specific operating taxonomic units (OTUs) highlighted an impact of the addition of benzodiazepines, a rapid resilience of the fungal community and an evolution of the bacterial community. It appeared that OTUs from the Brevibacillus genus were more abundant at the beginning of the biodegradation process, for diazepam and oxazepam conditions. Additionally, Tax4Fun tool was applied to 16S rRNA gene sequencing data to infer on the evolution of specific metabolic functions during biodegradation. It finally appeared that the microbial community in soils frequently exposed to water from WWTP, potentially containing CECs such as diazepam and oxazepam, may be adapted to the degradation of persistent contaminants.

Intercrop mulch affects soil biology and microbial diversity in rainfed transgenic Bt cotton hybrids

Growing live mulch between the wide-row spaced transgenic Bt cotton hybrids is a low-cost option to control weeds compared to the use of plastic mulch. However, nothing is known about their effects on soil biology. Therefore, soil samples were collected from a long-term field study (2014-15 to 2018-19) to investigate the soil biological activities as well as the microbial diversity (soil metagenomic analysis). In general, mulching enhanced soil biological activity and influenced the microbial diversity in Bt-cotton. Mulch of sunnhemp (Crotalaria juncea L.), desmodium (Desmodium triflorum L.), sorghum (Sorghum bicolor L.) and plastic sheet recorded significantly higher soil biological activities such as, basal respiration, microbial biomass carbon, and soil enzymes than the other mulch treatments. Aromatic crops (bitter cumin (Centratherum anthelminticum (L.) Kuntze), carom (Trachyspermum ammi (L.) Sprague ex Turrill), coriander (Coriandrum sativum L.), fennel (Foeniculum vulgare Mill.), and fenugreek (Trigonella foenum-graecum L.) had a significant adverse effect on soil biological activity compared to the farmers' practice (no mulch or intercrop). The rarefaction curves as a measure of alpha diversity indicated higher species richness in plastic and newspaper sheet mulch treatments compared to the intercrop mulch. The soil metagenome data indicated Proteobacteria (28%-36%), Actinobacteria (10%-35%), and Acidobacteria (10%-26%) were highly abundant phyla in the mulch treatments. The phyla, Chloroflexi (4%-5%), Gemmatimonadetes (2%-6%), Planctomycetes (2%-4%), and Bacteroidetes (2%-3%) were recorded at lower frequencies in all mulch treatments. The sunnhemp and newspaper mulch treatments recorded low frequency (0.06%-0.07%) of the fungal phyla, Ascomycota. Compared to the bare soil, mulching positively improves soil biological activity. Furthermore, our study identifies some crops that could be grown as an intercrop with a viewpoint to improve soil biology and provide an alternative to the expensive plastic mulch.

Effects of potassium fulvic acid and potassium humate on microbial biodiversity in bulk soil and rhizosphere soil of Panax ginseng

Potassium fulvic acid (BSFA) and potassium humate (KHM), as organic fertilizers, can improve soil structure, increase soil nutrient levels and prevent plant diseases. However, knowledge is limited regarding how BSFA and KHM influence soil microbial communities and the interrelationships between community members associated with Panax ginseng. Soil pH and nutrient content increased significantly as a result of the addition of BSFA and KHM. The pH, NH₄⁺-N, NO₃^--N, AP and AK increased by 1.72 %-5.55 %, 70.09 %-108.39 %, 35.38 %-216.20 %, 1.21 %-14.19 % and 3.40 %-5.94 %, respectively, in the BSFA and KHM treatments. The soil nutrient increase may be related to Micrococcaceae and arbuscular mycorrhizal fungi (AMF). The structure of the microbial community also changed radically from that of the control group, and Chloroflexi (2.69 %-3.15 %), Actinobacteria (4.33 %-7.53 %) and Acidobacteria (9.44 %-11.62 %) were the dominant microorganisms at the phylum level in bacteria. In contrast, the dominant fungi at the phylum level were Ascomycota (77.39 %-78.08 %), Glomeromycota (0.36 %-2.68), Olpidiomycota (0.02 %-3.78 %) and Basidiomycota (0.80 %-1.17 %). Fusarium oxysporum and Ascomycota were biomarkers for BSFA and KHM, which may be related to pathogenic bacteria. Network analysis revealed that the association among members of the soil microbial community was more positive than negative following application of KHM, and more positive (62.5 %) than negative (37.5 %) correlations were observed between bacteria, whereas the fungal community exhibited more positive (97.3 %) than negative (2.7 %) correlations. PICRUST predicted the microbial function of adding KHM and BSFA to the soil, and these pathways mainly belong to the degradation and metabolism of organic matter, saprophytic organisms and plant pathogens. In summary, our study demonstrated that the addition of BSFA and KHM increased the nutrients in the ginseng soil and reshaped the microbial function in soils, providing a theoretical foundation for soil improvement and biological control of ginseng diseases. However, due to the limitations of greenhouse cultivation, additional long-term experiments on farmland with different climate changes are recommended.

Soil microbial community and association network shift induced by several tall fescue cultivars during the phytoremediation of a petroleum hydrocarbon-contaminated soil

Biodegradation of soil contaminants may be promoted near plant roots due to the "rhizosphere effect" which may enhance microbial growth and activity. However, the effects of different plant cultivars within a single species on degradation remains unclear. Here, we evaluated the removal of soil total petroleum hydrocarbons (TPHs) by ten different cultivars of tall fescue grass (Festuca arundinacea L.) and their associated rhizosphere microbiomes. TPH removal efficiency across the ten different cultivars was not significantly correlated with plant biomass. Rhizing Star and Greenbrooks cultivars showed the maximum (76.6%) and minimum (62.2%) TPH removal efficiencies, respectively, after 120 days. Significant differences were observed between these two cultivars in the composition of rhizosphere bacterial and fungal communities, especially during the early stages (day 30) of remediation but the differences decreased later (day 90). Putative petroleum-degrading bacterial and fungal guilds were enriched in the presence of tall fescue. Moreover, the complexity of microbial networks declined in treatments with higher TPH removal efficiency. The relative abundances of saprotrophic fungi and putative genes alkB and C12O in bacetria involved in petroleum degradation increased, especially in the presence of Rhizing Star cultivar, and this was consistent with the TPH removal efficiency results. These results indicate the potential of tall fescue grass cultivars and their associated rhizosphere microbiomes to phytoremediate petroleum hydrocarbon-contaminated soils.

Farming systems influence the compositional, structural, and functional characteristics of the sugarcane-associated microbiome

Sugarcane (Saccharum spp.) has been produced worldwide as a relevant source of food and sustainable energy. However, the constant need to increase crop yield has led to excessive use of synthetic agrochemical inputs such as inorganic fertilizers, herbicides, and pesticides in plant cultures. It is known that these conventional practices can lead to deleterious effects on health and the environment. Organic farming emerges as a sustainable alternative to conventional systems; however, farm management influences in plant-associated microbiomes remain unclear. Here, the aim is to identify the effects of farming systems on the sugarcane microbiota. To address this issue, we sampled the microbiota from soils and plants under organic and conventional farming from two crop fields in Brazil. Then, we evaluated their compositional, structural, and functional traits through amplification and sequencing of phylogenetic markers of bacteria (16S rRNA gene, V3-V4 region) and fungi (Internal Transcribed Spacer - ITS2). The data processing and analyses by the DADA2 pipeline revealed 12,839 bacterial and 3,222 fungal sequence variants. Moreover, differences between analogous niches were detected considering the contrasting farming systems, with samples from the conventional system showing a slightly greater richness and diversity of microorganisms. The composition is also different between the farming systems, with 389 and 401 differentially abundant taxa for bacteria and fungi, respectively, including taxa capable of promoting plant growth. The microbial co-occurrence networks showed structural changes in microbial communities, where organic networks were more cohesive since they had closer taxa and less modularity by niches. Finally, the functional prediction revealed enriched metabolic pathways, including the increased presence of antimicrobial resistance in the conventional farming system. Taken together, our findings reveal functional, structural, and compositional adaptations of the microbial communities associated with sugarcane plants in the field, according to farming management. With this, we point out the need to unravel the mechanisms driving these adaptations.

The impact of antimicrobials on the efficiency of methane fermentation of sewage sludge, changes in microbial biodiversity and the spread of antibiotic resistance

The study was designed to simultaneously evaluate the influence of high doses (512-1024 µg/g) the most commonly prescribed antimicrobials on the efficiency of anaerobic digestion of sewage sludge, qualitative and quantitative changes in microbial consortia responsible for the fermentation process, the presence of methanogenic microorganisms, and the fate of antibiotic resistance genes (ARGs). The efficiency of antibiotic degradation during anaerobic treatment was also determined. Metronidazole, amoxicillin and ciprofloxacin exerted the greatest effect on methane fermentation by decreasing its efficiency. Metronidazole, amoxicillin, cefuroxime and sulfamethoxazole were degraded in 100%, whereas ciprofloxacin and nalidixic acid were least susceptible to degradation. The most extensive changes in the structure of digestate microbiota were observed in sewage sludge exposed to metronidazole, where a decrease in the percentage of bacteria of the phylum Bacteroidetes led to an increase in the proportions of bacteria of the phyla Firmicutes and Proteobacteria. The results of the analysis examining changes in the concentration of the functional methanogen gene (mcrA) did not reflect the actual efficiency of methane fermentation. In sewage sludge exposed to antimicrobials, a significant increase was noted in the concentrations of β-lactam, tetracycline and fluoroquinolone ARGs and integrase genes, but selective pressure was not specific to the corresponding ARGs.

Identification and Differentiation of Pseudomonas Species in Field Samples Using an rpoD Amplicon Sequencing Methodology

Species of the genus Pseudomonas are used for several biotechnological purposes, including plant biocontrol and bioremediation. To exploit the Pseudomonas genus in environmental, agricultural, or industrial settings, the organisms must be profiled at the species level as their bioactivity potential differs markedly between species. Standard 16S rRNA gene amplicon profiling does not allow for accurate species differentiation. Thus, the purpose of this study was to develop an amplicon-based high-resolution method targeting a 760-nucleotide (nt) region of the rpoD gene enabling taxonomic differentiation of Pseudomonas species in soil samples. The method was benchmarked on a 16-member Pseudomonas species mock community. All 16 species were correctly and semiquantitatively identified using rpoD gene amplicons, whereas 16S rRNA V3-V4 amplicon sequencing only correctly identified one species. We analyzed the Pseudomonas profiles in 13 soil samples in northern Zealand, Denmark, where samples were collected from grassland (3 samples) and agriculture soil (10 samples). Pseudomonas species represented up to 0.7% of the 16S rRNA gene abundance, of which each sampling site contained a unique Pseudomonas composition. Thirty culturable Pseudomonas strains were isolated from each grassland site and 10 from each agriculture site and identified by Sanger sequencing of the rpoD gene. In all cases, the rpoD amplicon approach identified more species than were found by cultivation, including hard-to-culture nonfluorescent pseudomonads, as well as more than were found by 16S rRNA V3-V4 amplicon sequencing. Thus, rpoD profiling can be used for species profiling of Pseudomonas, and large-scale prospecting of bioactive Pseudomonas may be guided by initial screening using this method.

IMPORTANCE A high-throughput sequencing-based method for profiling of Pseudomonas species in soil microbiomes was developed and identified more species than 16S rRNA gene sequencing or cultivation. Pseudomonas species are used as biocontrol organisms and plant growth-promoting agents, and the method will allow tracing of specific species of Pseudomonas as well as enable screening of environmental samples for further isolation and exploitation.

Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.

Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.

Organic micropollutant removal in full-scale rapid sand filters used for drinking water treatment in The Netherlands and Belgium

Biological treatment processes have the potential to remove organic micropollutants (OMPs) during water treatment. The OMP removal capacity of conventional drinking water treatment processes such as rapid sand filters (RSFs), however, has not been studied in detail. We investigated OMP removal and transformation product (TP) formation in seven full-scale RSFs all treating surface water, using high-resolution mass spectrometry based quantitative suspect and non-target screening (NTS). Additionally, we studied the microbial communities with 16S rRNA gene amplicon sequencing (NGS) in both influent and effluent waters as well as the filter medium, and integrated these data to comprehensively assess the processes that affect OMP removal. In the RSF influent, 9 to 30 of the 127 target OMPs were detected. The removal efficiencies ranged from 0 to 93%. A data-driven workflow was established to monitor TPs, based on the combination of NTS feature intensity profiles between influent and effluent samples and the prediction of biotic TPs. The workflow identified 10 TPs, including molecular structure. Microbial community composition analysis showed similar community composition in the influent and effluent of most RSFs, but different from the filter medium, implying that specific microorganisms proliferate in the RSFs. Some of these are able to perform typical processes in water treatment such as nitrification and iron oxidation. However, there was no clear relationship between OMP removal efficiency and microbial community composition. The innovative combination of quantitative analyses, NTS and NGS allowed to characterize real scale biological water treatments, emphasizing the potential of bio-stimulation applications in drinking water treatment.

High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests

Microbial communities in the immediate environment of socialized invertebrates can help to suppress pathogens, in part by synthesizing bioactive natural products. Here we characterized the core microbiomes of three termite species (genus Coptotermes) and their nest material to gain more insight into the diversity of termite-associated bacteria. Sampling a healthy termite colony over time implicated a consolidated and highly stable microbiome, pointing toward the fact that beneficial bacterial phyla play a major role in termite fitness. In contrast, there was a significant shift in the composition of the core microbiome in one nest during a fungal infection, affecting the abundance of well-characterized Streptomyces species (phylum Actinobacteria) as well as less-studied bacterial phyla such as Acidobacteria. High-throughput cultivation in microplates was implemented to isolate and identify these less-studied bacterial phylogenetic group. Amplicon sequencing confirmed that our method maintained the bacterial diversity of the environmental samples, enabling the isolation of novel Acidobacteriaceae and expanding the list of cultivated species to include two strains that may define new species within the genera Terracidiphilus and Acidobacterium.

Differences in metabolic potential between particle-associated and free-living bacteria along Pearl River Estuary

Particulate organic matter (POM) in aquatic ecosystem is critical for biogeochemical cycling and host distinct communities of microbes, compared to its surrounding water. In this study, the structures and functional potentials of microbial communities associated with particles or free-living in water samples from the Pearl River Estuary were investigated using 16S rRNA gene sequencing and GeoChip 5.0 analysis. Significant differences in the community structure and genetic functional potentials between particle-associated bacteria and free-living bacteria were observed across all eight sampling sites. In particle-associated bacteria communities, Rhodobacteraceae and Flavobacteriaceae were more abundant, while SAR11 clade and SAR86 clade were the most abundant in free-living bacteria communities. The richness and abundance of functional genes involved in nutrient cycling and stress response, including carbon degradation, nitrogen fixation, DMSP degradation, and polyphosphate degradation, were much higher in particle-associated bacteria compared with free-living bacteria. Thus, the particle-associated bacteria seem to play a much more important role in the biogeochemical cycles than free-living bacteria. In conclusion, the results from this study highlight the central role played by particle-associated bacteria in structuring microbial assemblages, and their importance for mediating biogeochemical cycling in the estuarine ecosystem.