Aquabacterium gen. nov., with description of Aquabacterium citratiphilum sp. nov., Aquabacterium parvum sp. nov. and Aquabacterium commune sp. nov., three in situ dominant bacterial species from the Berlin drinking water system

Oxygen-dependent biofilm dynamics in leaf decay: an in vitro analysis

Biofilms are important in the natural process of plant tissue degradation. However, fundamental knowledge of biofilm community structure and succession on decaying leaves under different oxygen conditions is limited. Here, we used 16S rRNA and ITS gene amplicon sequencing to investigate the composition, temporal dynamics, and community assembly processes of bacterial and fungal biofilms on decaying leaves in vitro. Leaves harvested from three plant species were immersed in lake water under aerobic and anaerobic conditions in vitro for three weeks. Biofilm-covered leaf samples were collected weekly and investigated by scanning electron microscopy. The results showed that community composition differed significantly between biofilm samples under aerobic and anaerobic conditions, though not among plant species. Over three weeks, a clear compositional shift of the bacterial and fungal biofilm communities was observed. The alpha diversity of prokaryotes increased over time in aerobic assays and decreased under anaerobic conditions. Oxygen availability and incubation time were found to be primary factors influencing the microbial diversity of biofilms on different decaying plant species in vitro. Null models suggest that stochastic processes governed the assembly of biofilm communities of decaying leaves in vitro in the early stages of biofilm formation and were further shaped by niche-associated factors.

Field evaluation of carbon injection method for in-situ biological denitrification in groundwater using geochemical and metataxonomic analyses

This study focuses on the bioremediation of nitrate-contaminated groundwater, which has become a significant environmental problem due to the increasing usage of fertilizers and sewage disposal. The nitrate reduction efficiencies of biological denitrification by injection of carbon source in a pilot-scale treatment system setup were investigated at a groundwater contamination site. The field test was conducted using acetate as a carbon source for 22 days to assess the nitrate reduction efficiencies of in-situ treatment. Geochemical parameters and microbial community analysis using next-generation sequencing were performed before and after carbon source injection. After 12 h of reaction time, nitrate concentration decreased from 31.6 to 4.2 mg-N/L at PC-2, and then remained stable at 3.9 mg-N/L. The nitrate reduction rate when acetate was injected was 29.0 mg-N/L/day. Aquabacterium commune, pseudomonas brassicacearum, dechloromonas denitrificans, and Massilia FAOS were dominant species after acetate injection. Predictive metabolic pathway analysis indicated that nitrate reduction metabolisms during injection of acetate were denitrification and assimilatory nitrate reduction to ammonium. The evaluated hazard quotient of nitrate-contaminated groundwater significantly decreased after acetate injection (non-carcinogenic risk decreased from 1.176 to 0.134 for children). This research could provide fundamental information for decision-makers in nitrate-contaminated groundwater quality protection and management.

New insights for tracking bacterial community structures in industrial wastewater from textile factories to surface water using phenotypic, 16S rRNA isolates identifications and high-throughput sequencing

Industrial wastewater can possibly change the microbial ecological environment. There are few studies that focus on the bacterial variety in textile wastewater effluents and after combination with domestic wastewater. Thus, this study aimed to determine dye degrading bacteria from textile wastewater and environmental water samples using cultural method followed by phenotypic using BIOLOG and genotypic identification (16S rRNA) for dye degrading isolates identifications. Moreover, the bacterial communities in three textile and four environmental samples using Illumina MiSeq high-throughput sequencing were investigated. The findings revealed that in textile water samples, the ratio of dye-degrading bacteria (DDB) to total bacterial counts (TBC) was 27%. The identified DDB genera by 16S rRNA based on the cultural approach were Citrobacter spp., Klebsiella spp., Enterobacter spp., Pseudomonas spp., and Aeromonas spp. Regarding to the metagenomics analyses, the environmental samples had 5,598 Operational Toxanomic Units (OTUs) more than textile wastewater samples (1,463 OTUs). Additionally, the most abundant phyla in the textile wastewater were Proteobacteria (24.45-94.83%), Bacteriodetes (0.5-44.84%) and Firmicutes (3.72-67.40%), while, Proteobacteria (30.8-76.3%), bacteroidetes (8.5-50%) and Acentobacteria (0.5-23.12%) were the most abundant phyla in the environmental samples. The maximum abundant bacteria at species level in environmental samples were Aquabacterium parvum (36.71%), Delftia tsuruhatensis (17.61%), Parabacteriodes chartae (15.39%) and Methylorubrum populi (7.51%) in El-Rahawy Drain water (RDW), River Nile water (RNW), wastewater (RWW) from WWTP in Zennin and El-Rahawy Drain sediment (RDS), respectively, whereas the maximum abundant bacteria at species level in textile wastewater were Alkalibacterium pelagium (34.11%), Enterobacter kobei (26.09%) and Chryseobacterium montanum (16.93%) in factory 1 (HBT) sample, SHB sample (before mixing with domestic wastewater) and SHB sample (after mixing with domestic wastewater), respectively. In conclusion, the microbial communities in textile wastewaters are similar to those in environmental samples at the phylum level but distinct at the genus and species levels because they are exposed to a wider range of environmental circumstances.

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.

Secondary microplastics formation and colonized microorganisms on the surface of conventional and degradable plastic granules during long-term UV aging in various environmental media

Recently, biodegradable plastics (BPs) as an alternative of conventional plastics have been widely advocated and applied. However, there is still a large research gap between the formation of secondary microplastics (MPs) and colonized microorganisms on their surface under long-term aging in different environments. In this study, the generation of secondary MPs and the formation of surface biofilms on the micro-sized (3-5 mm) biodegradable plastic poly (butyleneadipate-co-terephthalate) (BP-PBAT) and conventional plastic polyvinyl chloride (CP-PVC) under long-term UV aging was investigated. The results showed that hundreds and even thousands of MPs (185.53 ± 85.73 items/g - 1473.27 ± 143.67 items/g) were generated by BP-PBAT and CP-PVC after aged for 90 days, and the abundance of MPs produced by BP-PBAT was significantly higher than that of CP-PVC. Moreover, the α diversities and detected OTU number of biofilm communities formed on MPs increased with MPs-aging. The genes related to the formation of biofilms was significantly expressed on aged MPs and the genes related to human pathogens and diseases were also detected in enriching on MPs surface. Overall, BPs may lead to greater ecological risks as it releases thousands of secondary MPs after being aged, and their environmental behavior needs to be further explored.

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome

Fresh potable water is an indispensable drink which humans consume daily in substantial amounts. Nonetheless, very little is known about the composition of the microbial community inhabiting drinking water or its impact on our gut microbiota. In the current study, an exhaustive shotgun metagenomics analysis of the tap water microbiome highlighted the occurrence of a highly genetic biodiversity of the microbial communities residing in fresh water and the existence of a conserved core tap water microbiota largely represented by novel microbial species, representing microbial dark matter. Furthermore, genome reconstruction of this microbial dark matter from water samples unveiled homologous sequences present in the faecal microbiome of humans from various geographical locations. Accordingly, investigation of the faecal microbiota content of a subject that daily consumed tap water for 3 years provides proof for horizontal transmission and colonization of water bacteria in the human gut.

Microbial Community Response to a Bioaugmentation Test to Degrade Trichloroethylene in a Fractured Rock Aquifer, Trenton, N.J

Bioaugmentation is a promising strategy for enhancing trichloroethylene (TCE) degradation in fractured rock. However, slow or incomplete biodegradation can lead to stalling at degradation byproducts such as 1,2-dichloroethene (cis-DCE) and vinyl chloride (VC). Over the course of 7 years, we examined the response of groundwater microbial populations in a bioaugmentation test where an emulsified vegetable oil solution (EOS®) and a dechlorinating consortium (KB-1®), containing the established dechlorinator Dehalococcoides, were injected into a TCE-contaminated fractured rock aquifer. Indigenous microbial communities responded within 2 days to added substrate and outcompeted KB-1®, and over the years of monitoring, several other notable turnover events were observed. Concentrations of ethene, the end product in reductive dechlorination, had the strongest correlations (p< 0.05) with members of Candidatus Colwellbacteria but their involvement in reductive dechlorination is unknown and warrants further investigation. Dehalococcoides never exceeded 0.6% relative abundance of groundwater microbial communities, despite its previously presumed importance at the site. Increased concentrations of carbon dioxide, acetic acid, and methane were positively correlated with increasing ethene concentrations; however, concentrations of cis-DCE and VC remained high by the end of the monitoring period suggesting preferential enrichment of indigenous partial dechlorinators over bioaugmented complete dechlorinators. This study highlights the importance of characterizing in situ microbial populations to understand how they can potentially enhance or inhibit augmented TCE degradation.

Are carbon water filters safe for private wells? Evaluating the occurrence of microbial indicator organisms in private well water treated by point-of-use activated carbon block filters

Point-of-use (POU) water treatment is highly relevant to private well users vulnerable to chemical contamination, but uncertainty remains around the effects of activated carbon based POU devices on the microbial quality of the treated water. In this study, under-sink activated carbon block water filters were installed in 17 homes relying on private well water in North Carolina. The influent and effluent water in each home was evaluated for bacterial and viral microbial indicator organisms monthly for five months. Multiple logistic regression was used to identify water quality and water usage variables that were significant predictors of each indicator organism occurring in the filter effluent. The odds of total coliforms occurring in the effluent decreased by 84% with each 1-log₁₀ increase in the influent HPC (p < 0.05), suggesting a protective effect by native heterotrophic bacteria, but increased by over 50 times with low cumulative water use (p < 0.05). The filters were not protective against coliphages in the influent and viral shedding may occur after periods of increased virus concentrations in the raw well water. Specific bacteria were also found to increase in the effluent, causing a shift in the bacterial community composition, although potential opportunistic pathogens were detected in both the influent and the effluent. Overall, under normal conditions of use, the filters tested in this study did not represent a significant additional risk for well users beyond the existing exposures from undisinfected well water alone.

Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin

Strain SJQ9^T, an aerobic bacterium isolated from a soil sample collected in Shanghai, PR China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, 30-35 °C and in the presence of 1 % (w/v) NaCl. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ9^T fell within the genus Aquabacterium. The closest phylogenetic relatives of strain SJQ9^T were Aquabacterium citratiphilum DSM 11900^T (98.6 % sequence similarity) and Aquabacterium commune DSM 11901^T (96.4 %). Cells of the strain were Gram-stain-negative, motile, non-spore-forming, rod-shaped and positive for oxidase activity and negative for catalase. The chemotaxonomic properties of strain SJQ9^T were consistent with those of the genus Aquabacterium: the major fatty acid was summed feature 3 (C_16 : 1  ω6c and/or C_16 : 1  ω7c). The isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 65.7 mol%. Strain SH9^T exhibited a DNA-DNA relatedness level of 34±2 % with A. citratiphilum DSM 11900^T and 28±3 % with A. commune DSM 11901^T. Based on the obtained data, strain SJQ9^T represents a novel species of the genus Aquabacterium, for which the name Aquabacterium soli sp. nov. is proposed. The type strain is SJQ9^T (=JCM 33106^T=CCTCC AB 2018284^T).

Evaluation of natural attenuation-potential and biogeochemical analysis in nitrate contaminated bedrock aquifers by carbon source injection

In this study, the natural attenuation potential and biogeochemical analysis of nitrate contaminated bedrock aquifers by injection of carbon sources was evaluated. The denitrification capacity was assessed by injecting different carbon sources (succinate, acetate, fumarate) into the groundwater. Acetate was identified as the optimum source of electron donors for microbial metabolic processes, as it improved the effect of nitrate removal and microbial activity in the groundwater. In addition, when acetate was injected with a C/N ratio = 2.1:1, the ratio of denitrifying bacteria was the greatest (C/N 2.1 (2.1%) > C/N 4.2 (1.9%) > C/N 7.0 (0.9%) > control (0.7%)). Reflecting the geochemical characteristics of the bedrock aquifer environment, acetate was injected into groundwater at the research site to activate biological heterotrophic denitrification. As a result, the nitrate reduction rate was 0.377 g-N/day (YP-3), while the rate in groundwater unaffected by acetate was significantly lower, at 0.028 g-N/day (YP-4) over the same reaction time. In particular, the ratio of Dechloromonas denitrificans sp., which is a representative denitrification bacteria involved in anaerobic reduction of nitrate, increased (before injection: 0.0089%, after injection: 1.3067%). Expression of the nosZ gene, which is involved in the denitrification pathway (N₂O → N₂), increased from 4.82 Log (gene copies L^-1) to 9.71 Log (gene copies L^-1). Together, these results demonstrate that denitrification in bedrock aquifers can be activated by injection of carbon sources and identified the genetic reason for that denitrification.

Organic and nitrogenous pollutants removal paths in vegetation activated sludge process (V-ASP) for decentralized wastewater treatment by using stable isotope technique

The organics (C) and nitrogenous (N) pollutants removal paths by functional units in vegetation-activated sludge process (V-ASP) were investigated by using stable isotope probing and high-throughput sequencing for the first time. V-ASP system displayed superior treatment performance compared to conventional activated sludge system, as manifested by its greater C and N removal efficiencies, higher abundance of denitrifying and heterotrophic functional Genus, and better resistance to low temperature. Isotope δ¹³C and δ¹⁵N were continuously accumulated in plant roots allocated in the V-ASP, where suspended sludge demonstrated obviously higher C and N enrichment rates compared to the rhizosphere sludge. The mass balance estimation showed that bacterial dissimilation was the dominant removal paths for C (54.13%) and N (47.53%). The underlying pollutants removal paths evidenced the advantageous of V-ASP that is a high feasible and promising approach for decentralized wastewater treatment process.

Side Effects of Pesticides and Metabolites in Groundwater: Impact on Denitrification

The impact of two pesticides (S-metolachlor and propiconazole) and their respective main metabolites (ESA-metolachlor and 1,2,4-triazole) on bacterial denitrification in groundwater was studied. For this, the denitrification activity and the bacterial diversity of a microbial community sampled from a nitrate-contaminated groundwater were monitored during 20 days in lab experiments in the presence or absence of pesticides or metabolites at 2 or 10 μg/L. The kinetics of nitrate reduction along with nitrite and N₂O production all suggested that S-metolachlor had no or only little impact, whereas its metabolite ESA-metolachlor inhibited denitrification by 65% at 10 μg/L. Propiconazole and 1,2,4-triazole also inhibited denitrification at both concentrations, but to a lesser extent (29–38%) than ESA-metolachlor. When inhibition occurred, pesticides affected the reduction of nitrate into nitrite step. However, no significant differences were detected on the abundance of nitrate reductase narG and napA genes, suggesting an impact of pesticides/metabolites at the protein level rather than on denitrifying bacteria abundance. 16S rRNA gene Illumina sequencing indicated no major modification of bacterial diversity in the presence or absence of pesticides/metabolites, except for ESA-metolachlor and propiconazole at 10 μg/L that tended to increase or decrease Shannon and InvSimpson indices, respectively. General growth parameters suggested no impact of pesticides, except for propiconazole at 10 μg/L that partially inhibited acetate uptake and induced a decrease in microbial biomass. In conclusion, pesticides and metabolites can have side effects at environmental concentrations on microbial denitrification in groundwater and may thus affect ecosystem services based on microbial activities.

Temperature management potentially affects carbon mineralization capacity and microbial community composition of a shallow aquifer

High-temperature aquifer thermal energy storage (HT-ATES) is a promising technique to reduce the CO2 footprint of heat supply in the frame of transitioning to renewable energies. However, HT-ATES causes temperature fluctuations in groundwater ecosystems potentially affecting important microbial-mediated ecosystem services. Hence, assessing the impact of increasing temperatures on the structure and functioning of aquifer microbiomes is crucial to evaluate potential environmental risks associated with HT-ATES. In this study, we investigated the effects of temperature variations (12-80°C) on microbial communities and their capacity to mineralize acetate in aerobically incubated sediment sampled from a pristine aquifer. Compared to natural conditions (12°C), increased acetate mineralization rates were observed at 25°C, 37°C and 45°C, whereas mineralization was decelerated at 60°C and absent at 80°C. Sequencing of 16S rRNA genes revealed that the bacterial diversity in acetate-amended and non-acetate-amended sediments decreased with rising temperatures. Distinct communities dominated by bacterial groups affiliated with meso- and thermophilic bacteria established at 45°C and 60°C, respectively, while the number of archaeal phylotypes decreased. The changes in microbial diversity observed at 45°C and 60°C indicate a potential loss of ecosystem functioning, functional redundancy and resilience, while heat storage at 80°C bears the risk of ecological collapse.

Aquabacterium terrae sp. nov., isolated from soil

A yellow-colored bacterial strain, designated S2^T was isolated from soil in South Korea. Cells of strain S2^T were strictly aerobic, Gram-stain-negative, motile with single polar flagellum, rod-shaped, oxidase and catalase-negative. Growth occurs at 10-37 °C (optimum, 28 °C), pH 5.0-9.0 (optimum, pH 6.5-7.0) and 0-3% NaCl (w/v). Strain S2^T consisted of summed feature 3 (iso-C_15:0 2-OH and/or C_16:1 ω7c), C_16:0 and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c) as major fatty acids. The sole respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine and an unidentified lipid. The 16S rRNA gene sequence analysis showed that strain S2^T is phylogenetically closest to Aquabacterium pictum W35^T (98.4% sequence similarity). The genome of strain S2^T was 8,039,486 bp with 56 scaffolds. The genome consisted of 10 putative biosynthetic gene clusters that are responsible for various secondary metabolites. Genomic DNA G + C content of strain S2^T was 69.4%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain S2^T and phylogenetically related taxa were ≤ 77.9 and ≤ 21.4%, and respectively. The results of genotypic and phenotypic data showed that strain S2^T could be distinguished from its phylogenetically related species and represents a novel species in the genus Aquabacterium, for which the name Aquabacterium terrae sp. nov. is proposed. The type strain is S2^T (= KCTC 72741 ^T = NBRC 114609 ^T).

Arsenic behavior in groundwater in Hanoi (Vietnam) influenced by a complex biogeochemical network of iron, methane, and sulfur cycling

The fate of arsenic (As) in groundwater is determined by multiple interrelated microbial and abiotic processes that contribute to As (im)mobilization. Most studies to date have investigated individual processes related to As (im)mobilization rather than the complex networks present in situ. In this study, we used RNA-based microbial community analysis in combination with groundwater hydrogeochemical measurements to elucidate the behavior of As along a 2 km transect near Hanoi, Vietnam. The transect stretches from the riverbank across a strongly reducing and As-contaminated Holocene aquifer, followed by a redox transition zone (RTZ) and a Pleistocene aquifer, at which As concentrations are low. Our analyses revealed fermentation and methanogenesis as important processes providing electron donors, fueling the microbially mediated reductive dissolution of As-bearing Fe(III) minerals and ultimately promoting As mobilization. As a consequence of high CH₄ concentrations, methanotrophs thrive across the Holocene aquifer and the redox transition zone. Finally, our results underline the role of SO₄^2--reducing and putative Fe(II)-/As(III)-oxidizing bacteria as a sink for As, particularly at the RTZ. Overall, our results suggest that a complex network of microbial and biogeochemical processes has to be considered to better understand the biogeochemical behavior of As in groundwater.

Specific enrichment of hydrocarbonclastic bacteria from diesel-amended soil on biochar particles

Biochar has been proposed as a suitable biostimulant for the remediation of hydrocarbon contamination, and also has the potential to act as a carrier for hydrocarbonoclastic microorganisms which could bioaugment endogenous microbial communities. However, the evidence regarding the biostimulatory effects of biochars on hydrocarbon bioremediation is somewhat equivocal, possibly due to variability of the physicochemical properties of biochar and soil across studies. Here, we use standard biochars with defined properties produced from softwood pellets (SWP) and rice husk (RH) at pyrolysis temperatures of 550 °C or 700 °C to test the effects of biochar amendment on microbial community composition and hydrocarbon degradation in soil microcosms contaminated with diesel oil. Combining this approach for the first time with specific analysis of microbial community composition using amplicon sequence variants (ASVs), we find that oil contamination causes extreme short-term loss of soil microbial diversity, and highly-specific selection of a limited set of genera defined by 13 ASVs. Biochar ameliorates the short-term loss of diversity, and in the longer term (9 weeks), changes community composition in a type-specific manner. The majority of the 13 selected ASVs are further enriched on biochar particles, although SWP biochars perform better than RH biochar in enrichment of putative hydrocarbonoclastic Aquabacterium spp. However, complete degradation of normal (n) alkanes from the aliphatic hydrocarbon fraction is prevented in the presence of biochar amendment, possibly due to their adsorption onto the char surface. Furthermore, we show that putative hydrocarbon degraders released from diesel-amended soil can subsequently be enriched to high levels on SWP biochar particles in growth medium supplemented with diesel oil as the sole carbon source; these include selected ASVs representing the genera Rhodococcus, Aquabacterium, and Cavicella. This work suggests that use of biochar pre-enriched with endogenous, conditionally-rare hydrocarbon degrading bacteria is a promising strategy for bioaugmentation of diesel-contaminated soils.

Early and differential bacterial colonization on microplastics deployed into the effluents of wastewater treatment plants

Microbial colonization of microplastics (MPs) in aquatic ecosystems is a well-known phenomenon; however, there is insufficient knowledge of the early colonization phase. Wastewater treatment plant (WWTP) effluents have been proposed as important pathways for MPs entry and transport in aquatic environments and are hotspots of bacterial pathogens and antibiotic resistance genes (ARGs). This study aimed at characterizing bacterial communities in the early stage of biofilm formation on seven different types of MPs deployed in two different WWTPs effluents as well as measuring the relative abundance of two ARGs (sulI and tetM) on the tested MPs. Illumina Miseq sequencing of the 16S rRNA showed significant higher diversity of bacteria on MPs in comparison with free-living bacteria in the WWTP effluents. β-diversity analysis showed that the in situ environment (sampling site) and hydrophobicity, to a lesser extent, had a role in the early bacterial colonization phase. An early colonization phase MPs-core microbiome could be identified. Furthermore, specific core microbiomes for each type of polymer suggested that each type might select early attachment of bacteria. Although the tested WWTP effluent waters contained antibiotic resistant bacteria (ARBs) harboring the sulI and tetM ARGs, MPs concentrated ARBs harboring the sulI gene but not tetM. These results highlight the relevance of the early attachment phase in the development of bacterial biofilms on different types of MP polymers and the role that different types of polymers might have facilitating the attachment of specific bacteria, some of which might carry ARGs.

Microbial Signatures in Deep CO2-Saturated Miocene Sediments of the Active Hartoušov Mofette System (NW Czech Republic)

The Hartoušov mofette system is a natural CO₂ degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO₂ on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO₂ blow out occurred at a depth of 78.5 meter below surface (mbs) suggesting a CO₂ reservoir associated with a deep low-permeable CO₂-saturated saline aquifer at the transition from Early Miocene terrestrial to lacustrine sediments. Past microbial communities were investigated by hopanoids and glycerol dialkyl glycerol tetraethers (GDGTs) reflecting the environmental conditions during the time of deposition rather than showing a signal of the current deep biosphere. The composition and distribution of the deep microbial community potentially stimulated by the upward migration of CO₂ starting during Mid Pleistocene time was investigated by intact polar lipids (IPLs), quantitative polymerase chain reaction (qPCR), and deoxyribonucleic acid (DNA) analysis. The deep biosphere is characterized by microorganisms that are linked to the distribution and migration of the ascending CO₂-saturated groundwater and the availability of organic matter instead of being linked to single lithological units of the investigated rock profile. Our findings revealed high relative abundances of common soil and water bacteria, in particular the facultative, anaerobic and potential iron-oxidizing Acidovorax and other members of the family Comamonadaceae across the whole recovered core. The results also highlighted the frequent detection of the putative sulfate-oxidizing and CO₂-fixating genus Sulfuricurvum at certain depths. A set of new IPLs are suggested to be indicative for microorganisms associated to CO₂ accumulation in the mofette system.

Hydrodynamic effect on biofouling of milli-labyrinth channel and bacterial communities in drip irrigation systems fed with reclaimed wastewater

The clogging of drippers due to the development of biofilms reduces the benefits and is an obstacle to the implementation of drip irrigation technology in a reclaimed water context. The narrow section and labyrinth geometry of the dripper channel results the development of a heterogeneous flow behaviours with the vortex zones which it enhance the fouling mechanisms. The objective of this study was to analyse the influence of the three dripper types, defined by their geometric and hydraulic parameters, fed with reclaimed wastewater, on the biofouling kinetics and the bacterial communities. Using optical coherence tomography, we demonstrated that the inlet of the drippers (mainly the first baffle) and vortex zones are the most sensitive area for biofouling. Drippers with the lowest Reynolds number and average cross-section velocity v (1 l·h^-1) were the most sensible to biofouling, even if detachment events seemed more frequent in this dripper type. Therefore, dripper flow path with larger v should be consider to improve the anti-clogging performance. In addition, the dripper type and the geometry of the flow path influenced the structure of the bacterial communities from dripper biofilms. Relative abundancy of filamentous bacteria belonging to Chloroflexi phylum was higher in 1 l·h^-1 drippers, which presented a higher level of biofouling. However, further research on the role of this phylum in dripper biofouling is required.

Bacterial community colonization on tire microplastics in typical urban water environments and associated impacting factors

Only limited information is available on bacterial communities' dynamics on tire microplastics in urban water environments. This study exploited 16S rDNA high-throughput sequencing to characterize bacterial communities on tire microplastics, using three different tire brands and tire sizes, in two typical urban water environments, including an influent pond of constructed wetland (CW) and its subsequent effluent into a landscape river (LR) during three different periods, namely, 1 month, 3 and 6 months. Results showed that the abundance of bacterial colonization on tire microplastics will increase over time. Proteobacteria, Bacteroidetes were the dominant bacteria at a phylum level, although they exhibited dynamic changes. At a genus level, the identifiable bacteria found in tire microplastics was generally the common bacteria in wastewater discharge, such as Aquabacterium and Denitratisoma. Additionally, alpha diversity showed no significant differences in bacterial communities at the same locations. While beta diversity showed that the bacterial communities on the tire microplastics in the two locations was different. BugBase revealed that tire microplastics could support pathogenic bacteria in urban water environments. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) indicated that the abundance of microorganisms associated with metabolism and degradation increased with time. Moreover, the ambient environmental factors were the main influencing factors of bacterial communities on tire microplastics. Herein, the contribution rate of nutrient salts (NO₂-N, NO₃-N, NH₄-N, CODcr) was approximately 63%, and that of environmental physical factors of T and pH was 50%. While physicochemical factors, including particle size, contact angle, element content only had a slight impact. Accordingly, tire microplastics, as an emerging environmental pollutant, can act as carries for bacterial colonization and propagation, particularly harmful microorganisms. Therefore, the obtained findings can provide new insight into potential risks of harmful microorganisms that colonize tire microplastics in urban water environments.

The influence mechanism of temperature on solid phase denitrification based on denitrification performance, carbon balance, and microbial analysis

In this work, the influence mechanism of temperature on solid phase denitrification (SPD) was investigated using a pilot-scale reactor supported with polycaprolactone (PCL). The results showed that under nitrate loads of ~31.5 mg N/(L·h), as temperature decreased from 30 °C to 13 °C, the nitrate removal efficiency declined from 94% to 57%. Furthermore, denitrification rate constants were input into Arrhenius equation and the resulting temperature coefficient was 1.04. Significantly nitrite accumulation and less effluent COD residue occurred at low-temperatures. Via stoichiometry, the sludge yield coefficient and COD demand for nitrate removal both increased as a function of increasing temperature; and were calculated at 20 °C as 0.069 g MLVSS/(g COD·d) and 3.265 g COD/g N, respectively. Carbon balance analysis indicated that the COD release rate (υ) at 30 °C was twice that at 13 °C. LEfSe analysis demonstrated that Desulfomicrobium, Desulfovibrio, and Meganema were abundant at low-temperature, while Simplicispira, Aquabacterium, and Acidovorax were enriched at high-temperature. Besides, carboxylesterase (PCL depolymerase) was more abundant at high-temperature, implying an association with a fast υ. Moreover, nar was enriched at low-temperature, while nir was depleted, which led to nitrite accumulation. These results provide reference for SPD design parameter estimation and/or optimal operation strategy.

Profiling native aquifer bacteria in a uranium roll-front deposit and their role in biogeochemical cycle dynamics: Insights regarding in situ recovery mining

A uranium-mineralized sandy aquifer, planned for mining by means of uranium in situ recovery (U ISR), harbors a reservoir of bacterial life that may influence the biogeochemical cycles surrounding uranium roll-front deposits. Since microorganisms play an important role at all stages of U ISR, a better knowledge of the resident bacteria before any ISR actuations is essential to face environmental quality assessment. The focus here was on the characterization of bacteria residing in an aquifer surrounding a uranium roll-front deposit that forms part of an ISR facility project at Zoovch Ovoo (Mongolia). Water samples were collected following the natural redox zonation inherited in the native aquifer, including the mineralized orebody, as well as compartments located both upstream (oxidized waters) and downstream (reduced waters) of this area. An imposed chemical zonation for all sensitive redox elements through the roll-front system was observed. In addition, high-throughput sequencing data showed that the bacterial community structure was shaped by the redox gradient and oxygen availability. Several interesting bacteria were identified, including sulphate-reducing (e.g. Desulfovibrio, Nitrospira), iron-reducing (e.g. Gallionella, Sideroxydans), iron-oxidizing (e.g. Rhodobacter, Albidiferax, Ferribacterium), and nitrate-reducing bacteria (e.g. Pseudomonas, Aquabacterium), which may also be involved in metal reduction (e.g. Desulfovibrio, Ferribacterium, Pseudomonas, Albidiferax, Caulobacter, Zooglea). Canonical correspondence analysis (CCA) and co-occurrence patterns confirmed strong correlations among the bacterial genera, suggesting either shared/preferred environmental conditions or the performance of similar/complementary functions. As a whole, the bacterial community residing in each aquifer compartment would appear to define an ecologically functional ecosystem, containing suitable microorganisms (e.g. acidophilic bacteria) prone to promote the remediation of the acidified aquifer by natural attenuation. Assessing the composition and structure of the aquifer's native bacteria is a prerequisite for understanding natural attenuation and predicting the role of bacterial input in improving ISR efficiency.

Aquabacterium lacunae sp. nov., isolated from a freshwater pond

A novel bacterial strain, designated KMB7^T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed cream colonies. Optimal growth occurred at 25 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain KMB7^T is affiliated with species in the genus Aquabacterium. The 16S rRNA gene sequence similarity indicated that strain KMB7^T is closely related to species within the genus Aquabacterium (95.2-97.6 % sequence similarity) and is most similar to A. fontiphilum CS-6^T (97.6 %), followed by A. parvum B6^T (97.5 %). The average nucleotide identity and digital DNA-DNA hybridization identity between strain KMB7^T and the closely related strains were 74.6-78.0 % and 19.0-21.2 %, respectively. The major fatty acids of strain KMB7^T were summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c), C_18 : 1  ω7c and C_16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unidentified phospholipids. The sole isoprenoid quinone was ubiquinone-8 (Q-8). Genomic DNA G+C content of strain KMB7^T was 65.4 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KMB7^T should be classified in a novel species of the genus Aquabacterium, for which the name Aquabacterium lacunae sp. nov. is proposed. The type strain is KMB7^T (=BCRC 81156^T=LMG 30924^T=KCTC 62867^T).

Saezia sanguinis gen. nov., sp. nov., a Betaproteobacteria member of order Burkholderiales, isolated from human blood

The taxonomic position of an unknown bacterial strain designated CNM695-12, isolated from the blood of an immunocompromised subject, was investigated via phenotypic, chemotaxonomic, genotypic and genomic analyses. Bacterial cells were determined to be Gram-stain-negative bacilli, aerobic, non-motile and non-spore-forming. The strain showed catalase activity but no oxidase activity. Optimal growth occurred at 37 °C, pH 7 and with 0-1 % NaCl. C_16 : 0, summed feature 8 (comprising C_18 : 1ω7c /C_18:1 ω6c), and C_18 : 1ω9c were the most abundant fatty acids, and ubiquinone 8 was the major respiratory quinone. The polar lipids present included phosphatidylglycerol, phosphatidylethanolamine and other aminophospholipids. The 16S rRNA gene sequence showed approximately 93.5 % similarity to those of different species with validly published names within the order Burkholderiales (e.g. Leptothrix mobilis Feox-1^T, Aquabacterium commune B8^T , Aquabacterium citratiphilum B4^T and Schlegelella thermodepolymerans K14^T). Phylogenetic analyses based on 16S rRNA gene sequences and concatenated alignments including the sequences for 107 essential proteins, revealed the strain to form a novel lineage close to members of the family Comamonadaceae. The highest average nucleotide identity and average amino acid identity values were obtained with Schlegelella thermodepolymerans K14^T (69.6 and 55.7 % respectively). The genome, with a size of 3.35 Mb, had a DNA G+C content of 52.4 mol% and encoded 3056 predicted genes, 3 rRNA, 1 transfer-messengerRNA and 51 tRNA. Strain CNM695-12 thus represents a novel species belonging to a novel genus within the order Burkholderiales, for which the name Saezia sanguinis gen. nov., sp. nov. is proposed. The type strain is CNM695-12^T (=DSM 104959^T=CECT 9208^T).

Comparison of Commercial Kits for Recovery and Analysis of Bacterial DNA From Fingerprints

In forensic science, fingerprints are a common source of evidentiary information. However, latent examination is not always successful and trace human DNA cannot always be obtained. Thus, examining the fingerprint microbiome may offer a suitable alternative to more traditional methods of forensic identification. The Zymo Research ZR Bacterial/Fungal DNA MicroPrep™ Kit, Qiagen QIAmp^® DNA Mini Kit, Promega Wizard^® Genomic DNA Purification Kit, and the MPBio FastDNA^® Spin Kit were compared for their ability to yield a sufficient amount of bacterial DNA for next-generation sequencing in order to obtain a microbiome profile. Prints were deposited onto slides, allowed to sit for up to 1 month, and total DNA isolated and quantified using each kit. The kit from Zymo Research yielded the most concentrated DNA sample (0.0084 ng/µL) in the least amount of time as compared to other kits examined. Although this amount of DNA was far below the recommended DNA concentration threshold recommended for next-generation sequencing, a microbiome profile was successfully obtained. As interest in using the microbiome of an individual as a forensic tool continues to increase, there is the possibility that the microbiome of a fingerprint could complement traditional human DNA profiling in the future. This study provides evidence that trace amounts of bacterial DNA from fingerprints is quantifiable and sufficient for microbiome analysis.

Enhanced hydrolysis-acidification of high-solids and low-organic-content sludge by biological thermal-alkaline synergism

In this study, a biological thermal-alkaline synergistic system was successfully established to enhance the hydrolysis-acidification efficiency of high-solids and low-organic-content sludge (HS-LOC-S). The results indicated that the highest hydrolysis rate was obtained at pH of 12 (52.62%) leading to the highest production of soluble chemical oxygen demand (SCOD) and soluble protein (SP). The highest acidification rate was observed at pH of 10 (32.15%), leading to the highest production of volatile fatty acids (VFAs). At pH of 10, average sludge size reduced by 24.60%, and the proportion of biodegradable dissolved organic matter (DOM) produced by synergistic system increased by 15.82%, when compared with those of raw sludge. Moreover, results of 16S rRNA clearly validated that the relative abundance of hydrolytic and acidogenic microbes (e.g. Tepidimicrobium, Coprothermobacter) abundantly enriched at pH of 10 (49.88%) was greatly higher than others, which was the main reason for its maximum VFAs accumulation.

Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria

A strictly aerobic, bacteriochlorophyll a-containing betaproteobacterium, designated strain W35^T, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds, and showed an in vivo absorption maximum at 871 nm in the near-infrared region, typical for the presence of bacteriochlorophyll a. The new bacterial strain is Gram-negative, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain W35^T was closely related to species in the genus Aquabacterium. The closest phylogenetic relatives of strain W35^T were Aquabacterium commune B8^T (97.9 % sequence similarity), Aquabacterium citratiphilum B4^T (97.2 %) and Aquabacterium limnoticum ABP-4^T (97.0 %). The major cellular fatty acids were C_{16  :  1}ω7c (50.4 %), C_{16  :  0} (22.7 %), summed feature 8 (C_{18  :  1}ω7c/C_{18  :  1}ω6c; 9.7 %), C_{18  :  3}ω6c (5.5 %), C_{12  :  0} (5.3 %) and C_{10  :  0} 3OH (2.7 %). The respiratory quinone was ubiquinone-8. Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA was 70.4 mol% (genome data) and 71.4 mol% (HPLC). The genome size of strain W35^T is 6.1 Mbp and average nucleotide identity analysis indicated genome similarities of strain W35^T and related Aquabacterium type strains to be 78-79 %. The results of polyphasic comparisons showed that strain W35^T was clearly distinguishable from other members of the genus Aquabacterium. Therefore, we propose a new species in the genus Aquabacterium, namely, Aquabacterium pictum sp. nov. The type strain is W35^T (=DSM 106757^T=NBRC 111963^T). The description of the genus Aquabacterium is also emended.

Occurrence and Succession of Bacterial Community in O3/BAC Process of Drinking Water Treatment

In the drinking water industry, a common advanced treatment process is comprised of treatment with ozone, followed by biological-activated carbon (O₃/BAC). However, the bacterial community formation and succession procedures associated with activated carbon have rarely been reported. In this study, the dynamics of bacterial communities at three different depths were investigated using a pilot-scale O₃/BAC filter. The average chemical oxygen demand (CODMn), turbidity removal and dissolved oxygen (DO) consumption rate of the filter were 26.43%, 16.57% and 16.4% during the operation period, respectively. Bacterial communities dominated by proteobacteria and Bacteroidetes attached on activated carbon were determined by polymerase chain reaction-density gradient gel electrophoresis (PCR-DGGE). Principal component analysis (PCA) revealed that the compositions and structures of bacterial communities in different layers clustered after fluctuation. A redundancy analysis (RDA) indicated that Ramlibacter henchirensis was positively correlated to chemical oxygen demand (COD_Mn) removal and nitrate-N removal, and Georgfuchsia toluolica also showed a positive correlation with COD_Mn removal. Aquabacterium parvum and Phaeobacterium nitratireducens were positively-correlated with turbidity removal. Pedobacter glucosidilyticus and Pseudomonas sp. were associated with high dissolved oxygen (DO) consumption. These results provide insight into the succession characteristics of the bacterial community of O₃/BAC treatment and the interactions of the bacterial community with filter operation performance.

Dietary supplementation of black soldier fly (Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron (Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets

The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture.

Bacterial Community of the Digestive Tract of the European Medicinal Leech (Hirudo verbana) from the Danube River

The digestive tract of medicinal leeches from commercial suppliers has been investigated previously and comprises of a relatively simple bacterial community. However, the microbiome of medicinal leeches collected directly from the natural habitat has not been examined. In this study, we characterized the bacterial community in the digestive tract (anterior crop, posterior crop, and intestine) of the European medicinal leech, Hirudo verbana, collected from the Danube river using culture-independent and culture-dependent approaches. Culture-independent approach confirmed that the digestive tract of H. verbana carries a relatively simple bacterial community with species richness in the individual samples ranging from 43 to164. The dominant bacterial taxon was Mucinivorans sp. (49.7% of total reads), followed by Aeromonas sp. (18.7% of total reads). Several low abundance taxa, new for H. verbana, such as Phreatobacter, Taibaiella, Fluviicola, Aquabacterium, Burkholderia, Hydrogenophaga, Wolinella, and unidentified Chitinophagia, were also detected. The aerobic culturing approach showed Aeromonas veronii (Proteobacteria), the known leech symbiont, as the most dominant taxon followed by several Pseudomonas and Acidovorax spp. No significant differences in the bacterial community composition were detected among different parts of the digestive tract of individual leeches. However, the overall composition of the bacterial community among individual specimen varied significantly and this is possibly due to differences in leech age, feeding status, and blood source. Our results showed that the core bacterial community of H. verbana collected from the natural habitat is similar to that reported from the digestive tract of commercially supplied leeches maintained in the laboratory.

Effects of tetrakis (hydroxymethyl) phosphonium sulfate pretreatment on characteristics of sewage sludge

Recently, tetrakis(hydroxymethyl)phosphonium sulfate (THPS) was found to play an important role in the sludge pretreatment process. However, the effects of THPS pretreatment on the characteristics of sewage sludge are still insufficiently understood. The properties of sludge after pretreatment with different concentrations of THPS were investigated in this study. The results showed that pH, dewatering ability, and particle size of sludge decreased with increase in THPS concentration. The volatile suspended solids (VSS) and total suspended solids (TSS) of sludge also decreased slightly with increase in THPS concentration. The specific oxygen uptake rate (SOUR) results suggested that lower THPS concentrations (≤1.87 mg/g VSS) enhanced the activity of sludge, but higher concentrations (≥1.87 mg/g VSS) inhibited it. Gram-negative bacteria with peritrichous flagellation (such as Pseudomonas, Escherichia, and Faecalibacterium) were extremely sensitive to THPS. The decrease in specific most probable numbers (MPNs) of pathogens (total coliforms and Escherichia coli) with the increase in THPS concentration also proved the sterilization ability of THPS in the sludge pretreatment process. Pretreatment of sludge with concentrations of THPS higher than 37.41 mg/g VSS would meet the pathogen requirements for land application of Class A biosolids.

Drip irrigation biofouling with treated wastewater: bacterial selection revealed by high-throughput sequencing

Clogging of drippers due to the development of biofilms weakens the advantages and impedes the implementation of drip irrigation technology. The objective of this study was to characterise the bacterial community of biofilms that develop in a drip irrigation system supplied with treated wastewater. High-throughput sequencing of 16S rRNA gene amplicons indicated that the bacterial community composition differed between drippers and pipes, mainly due to changes in the abundance of the genus Aquabacterium. Cyanobacteria were found to be involved in the biological fouling of drippers. Moreover, bacterial genera including opportunistic pathogenic bacteria such as Legionella and Pseudomonas were more abundant in dripper and pipe biofilms than in the incoming water. Some genera such as Pseudomonas were mostly recovered from drippers, while others (ie Bacillus, Brevundimonas) mainly occurred in pipes. Variations in the hydraulic conditions and properties of the materials likely explain the shift in bacterial communities observed between pipes and drippers.

Thermal Stability of a Mercuric Reductase from the Red Sea Atlantis II Hot Brine Environment as Analyzed by Site-Directed Mutagenesis

The lower convective layer (LCL) of the Atlantis II brine pool of the Red Sea is a unique environment in terms of high salinity, temperature, and high concentrations of heavy metals. Mercuric reductase enzymes functional in such extreme conditions could be considered a potential tool in the environmental detoxification of mercurial poisoning and might alleviate ecological hazards in the mining industry. Here, we constructed a mercuric reductase library from Atlantis II, from which we identified genes encoding two thermostable mercuric reductase (MerA) isoforms: one is halophilic (designated ATII-LCL) while the other is not (designated ATII-LCL-NH). The ATII-LCL MerA has a short motif composed of four aspartic acids (4D414-417) and two characteristic signature boxes that played a crucial role in its thermal stability. To further understand the mechanism behind the thermostability of the two studied enzymes, we mutated the isoform ATII-LCL-NH and found that the substitution of 2 aspartic acids (2D) at positions 415 and 416 enhanced the thermal stability, while other mutations had the opposite effect. The 2D mutant showed superior thermal tolerance, as it retained 81% of its activity after 10 min of incubation at 70°C. A three-dimensional structure prediction revealed newly formed salt bridges and H bonds in the 2D mutant compared to the parent molecule. To the best of our knowledge, this study is the first to rationally design a mercuric reductase with enhanced thermal stability, which we propose to have a strong potential in the bioremediation of mercurial poisoning.IMPORTANCE The Red Sea is an attractive environment for bioprospecting. There are 25 brine-filled deeps in the Red Sea. The Atlantis II brine pool is the biggest and hottest of such hydrothermal ecosystems. We generated an environmental mercuric reductase library from the lowermost layer of the Atlantis II brine pool, in which we identified two variants of the mercuric reductase enzyme (MerA). One is the previously described halophilic and thermostable ATII-LCL MerA and the other is a nonhalophilic relatively less thermostable enzyme, designated ATII-LCL-NH MerA. We used the ATII-LCL-NH enzyme as a parent molecule to locate the amino acid residues involved in the noticeably higher thermotolerance of the homolog ATII-LCL MerA. Moreover, we designed a novel enzyme with superior thermal stability. This enzyme might have strong potential in the bioremediation of mercuric toxicity.

Succession Patterns and Physical Niche Partitioning in Microbial Communities from Subsurface Coal Seams

The subsurface represents a largely unexplored frontier in microbiology. Here, coal seams present something of an oasis for microbial life, providing moisture, warmth, and abundant fossilized organic material. Microbes in coal seams are thought to syntrophically mobilize fossilized carbon from the geosphere to the biosphere. Despite the environmental and economic importance of this process, little is known about the microbial ecology of coal seams. In the current study, ecological succession and spatial niche partitioning are explored in three coal seam microbial communities. Scanning electron microscopic visualization and 16S rRNA sequencing track changes in microbial communities over time, revealing distinct attached and planktonic communities displaying patterns of ecological succession. Attachment to the coal surface is biofilm mediated on Surat coal, whereas microbes on Sydney and Gunnedah coal show different attachment processes. This study demonstrates that coal seam microbial communities undergo spatial niche partitioning during periods of succession as microbes colonize coal environments.

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Coal surfaces and waters have distinctly different microbial communities

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Microbes attach to coal surfaces via multiple adhesion strategies

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Adhesion strategies include biofilm formation and direct cell attachment

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Coal microbe succession patterns provide insights into possible community roles

Prevalence and transmission of antibiotic resistance and microbiota between humans and water environments

The transmission routes for antibiotic resistance genes (ARGs) and microbiota between humans and water environments is poorly characterized. Here, we used high-throughput qPCR analyses and 16S rRNA gene sequencing to examine the occurrence and abundance of antibiotic resistance genes and microbiota in both healthy humans and associated water environments from a Chinese village. Humans carried the most diverse assemblage of ARGs, with 234 different ARGs being detected. The total abundance of ARGs in feces, on skin, and in the effluent from domestic sewage treatment systems were approximately 23, 2, and 7 times higher than their abundance in river samples. In total, 53 ARGs and 28 bacteria genera that were present in human feces could also be found in the influent and effluent of rural sewage treatment systems, and also downstream of the effluent release point. We identified the bacterial taxa that showed a significant association with ARGs (P < 0.01, r > 0.8) by network analysis, supporting the idea that these bacteria could carry some ARGs and transfer between humans and the environment. Analysis of ARGs and microbiota in humans and in water environments helps to define the transmission routes and dynamics of antibiotic resistance within these environments. This study highlights human contribution to the load of ARGs into the environment and suggests means to prevent such dissemination.

Microbial subnetworks related to short-term diel O2 fluxes within geochemically distinct freshwater wetlands

Oxygen (O2) concentrations often fluctuate over diel timescales within wetlands, driven by temperature, sunlight, photosynthesis and respiration. These daily fluxes have been shown to impact biogeochemical transformations (e.g. denitrification), which are mediated by the residing microbial community. However, little is known about how resident microbial communities respond to diel physical and chemical fluxes in freshwater wetland ecosystems. In this study, total microbial (bacterial and archaeal) community structure was significantly related to diel time points in just one out of four distinct freshwater wetlands sampled. This suggests that daily environmental shifts may influence wetlands differentially based upon the resident microbial community and specific physical and chemical conditions of a freshwater wetland. When exploring the microbial communities within each wetland at finer resolutions, subcommunities of taxa within two wetlands were found to correspond to fluctuating O2 levels. Microbial taxa that were found to be susceptible to fluctuating O2 levels within these subnetworks may have intimate ties to metabolism and/or diel redox cycles. This study highlights that freshwater wetland microbial communities are often stable in community structure when confronted with short-term O2 fluxes; however, specialist taxa may be sensitive to these same fluxes.

Aquabacterium tepidiphilum sp. nov., a moderately thermophilic bacterium isolated from a hot spring

A Gram-stain-negative, aerobic, non-spore-forming and rod-shaped bacterium, designated YIM 730274^T, was isolated from a sediment sample collected from a hot spring located in Tibet, PR China, and was characterized by using a polyphasic taxonomy approach. Cells were motile by means of a polar flagellum. The strain was oxidase- and catalase-positive, and contained polyalkanoates and polyphosphate as storage polymers. Growth occurred at 25-50 °C, at pH 6.0-8.5 and with 0.5-1.0 % NaCl. The major fatty acids (>10 %) were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The known polar lipids comprised of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine. The isoprenoid quinone was Q-8. The G+C content of genomic DNA was 70.7 mol%. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the strain forms a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Aquabacterium in the class Betaproteobacteria. The most closely related phylogenetic neighbours were Aquabacterium limnoticumABP-4^T (97.8 % 16S rRNA gene sequence identity) and Aquabacterium communeB8^T (97.2 % 16SrRNA gene sequence identity). DNA-DNA relatedness values between YIM 730274^T and A. limnoticum KCTC 23306^T (46.4±0.4 %) and A. commune DSM 11901^T (42.2±1.2 %) were well below the 70 % limit for species identification. YIM 730274^T was distinguishable from other members of the genus Aquabacterium by the differences in phenotypic, chemotaxonomic and genotypic characteristics. YIM 730274^T merits recognition as a representative of a novel species of the genus Aquabacterium. It is proposed that the isolate should be classified in the genus Aquabacterium as representing a novel species, Aquabacteriumtepidiphilum sp. nov. The type strain is YIM 730274^T (=KCTC 52716^T=CCTCC AB 2016295^T).

Functional evaluation of pollutant transformation in sediment from combined sewer system

In this study, a pilot combined sewer system was constructed to characterize the pollutant transformation in sewer sediment. The results showed that particulate contaminants deposited from sewage could be transformed into dissolved matter by distinct pollutant transformation pathways. Although the oxidation-reduction potential (ORP) was varied from -80 mV to -340 mV in different region of the sediment, the fermentation was the dominant process in all regions of the sediment, which induced hydrolysis and decomposition of particulate contaminants. As a result, the accumulation of dissolved organic matter and the variation of ORP values along the sediment depth led to the depth-dependent reproduction characteristics of methanogens and sulfate-reducing bacteria, which were existed in the middle and deep layer of the sediment respectively. However, the diversity of nitrifying and polyphosphate-accumulating bacteria was low in sewer sediment and those microbial communities showed a non-significant correlation with nitrogen and phosphorus contaminants, which indicated that the enrichment of nitrogen and phosphorus contaminants was mainly caused by physical deposition process. Thus, this study proposed a promising pathway to evaluate pollutant transformation and can help provide theoretical foundation for urban sewer improvement.

Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters

BACKGROUND

Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown.

RESULTS

We performed a multifaceted analysis of microbiota and DOM diversity in 12 natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM.

CONCLUSIONS

The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.

Bacterial plasmid-mediated quinolone resistance genes in aquatic environments in China

Emerging antimicrobial resistance is a major threat to human’s health in the 21^st century. Understanding and combating this issue requires a full and unbiased assessment of the current status on the prevalence of antimicrobial resistance genes and their correlation with each other and bacterial groups. In aquatic environments that are known reservoirs for antimicrobial resistance genes, we were able to reach this goal on plasmid-mediated quinolone resistance (PMQR) genes that lead to resistance to quinolones and possibly also to the co-emergence of resistance to β-lactams. Novel findings were made that qepA and aac-(6′)-Ib genes that were previously regarded as similarly abundant with qnr genes are now dominant among PMQR genes in aquatic environments. Further statistical analysis suggested that the correlation between PMQR and β-lactam resistance genes in the environment is still weak, that the correlations between antimicrobial resistance genes could be weakened by sufficient wastewater treatment, and that the prevalence of PMQR has been implicated in environmental, pathogenic, predatory, anaerobic, and more importantly, human symbiotic bacteria. This work provides a comprehensive analysis of PMQR genes in aquatic environments in Jinan, China, and provides information with which combat with the antimicrobial resistance problem may be fought.

Improvement of biological nitrogen removal with nitrate-dependent Fe(II) oxidation bacterium Aquabacterium parvum B6 in an up-flow bioreactor for wastewater treatment

Aquabacterium parvum strain B6 exhibited efficient nitrate-dependent Fe(II) oxidation ability using nitrate as an electron acceptor. A continuous up-flow bioreactor that included an aerobic and an anoxic section was constructed, and strain B6 was added to the bioreactor as inocula to explore the application of microbial nitrate-dependent Fe(II) oxidizing (NDFO) efficiency in wastewater treatment. The maximum NRE (anoxic section) and TNRE of 46.9% and 79.7%, respectively, could be obtained at a C/N ratio of 5.3:1 in the influent with HRT of 17. Meanwhile, the taxonomy composition of the reactor was assessed, as well. The NDFO metabolism of strain B6 could be expected because of its relatively dominant position in the anoxic section, whereas potential heterotrophic nitrification and aerobic denitrification developed into the prevailing status in the aerobic section after 50days of continuous operation.

High-rate activated sludge communities have a distinctly different structure compared to low-rate sludge communities, and are less sensitive towards environmental and operational variables

High-rate activated sludge processes allow for the recovery of organics and energy from wastewaters. These systems are operated at a short sludge retention time and high sludge-specific loading rates, which results in a higher sludge yield and better digestibility than conventional, low-rate activated sludge. Little is known about the microbial ecology of high-rate systems. In this work, we address the need for a fundamental understanding of how high-rate microbial communities differ from low-rate communities. We investigated the high-rate and low-rate communities in a sewage treatment plant in relation to environmental and operational variables over a period of ten months. We demonstrated that (1) high-rate and low-rate communities are distinctly different in terms of richness, evenness and composition, (2) high-rate community dynamics are more variable and less shaped by deterministic factors compared to low-rate communities, (3) sub-communities of continuously core and transitional members are more shaped by deterministic factors than the continuously rare members, both in high-rate and low-rate communities, and (4) high-rate community members showed a co-occurrence pattern similar to that of low-rate community members, but were less likely to be correlated to environmental and operational variables. These findings provide a basis for further optimization of high-rate systems, in order to facilitate resource recovery from wastewater.

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor

Intense rainfall is one of the most serious and common natural events, causing the excessive inflow of rainwater into wastewater treatment plants. However, little is known about the impacts of rainwater dilution on the structure and function of the sludge microorganisms. Here, high-throughput sequencing of 16S ribosomal RNA (rRNA) genes was implemented to describe the microbial community dynamics during the simulated intense rainfall situation (event i) in which approximately 45 % of the sludge biomass was artificially overflowed by massive water supply in a pilot-scale membrane bioreactor. Thereafter, we investigated the functional and structural responses of the perturbed microbial communities to subsequent conditional changes, i.e., an increase in organic loading rate from 225 to 450 mg chemical oxygen demand (COD) l(-1) day(-1) (event ii) and an addition of a microbiota activator (event iii). Due to the event i, the COD removal declined to 78.2 %. This deterioration coincided with the decreased microbial diversity and the proliferation of the oligotrophic Aquabacterium sp. During the succeeding events ii and iii, the sludge biomass increased and the COD removal became higher (86.5-97.4 %). With the apparent recovery of the reactor performance, microbial communities became diversified and the compositions dynamically changed. Notably, various bacterial micropredators were highly enriched under the successive conditions, most likely being involved in the flexible reorganization of microbial communities. These results indicate that the activated sludge harbored functionally redundant microorganisms that were able to thrive and proliferate along with the conditional changes, thereby contributing to the functional maintenance of the membrane bioreactor.

A Diverse Community of Metal(loid) Oxide Respiring Bacteria Is Associated with Tube Worms in the Vicinity of the Juan de Fuca Ridge Black Smoker Field

Epibiotic bacteria associated with tube worms living in the vicinity of deep sea hydrothermal vents of the Juan de Fuca Ridge in the Pacific Ocean were investigated for the ability to respire anaerobically on tellurite, tellurate, selenite, selenate, metavanadate and orthovanadate as terminal electron acceptors. Out of 107 isolates tested, 106 were capable of respiration on one or more of these oxides, indicating that metal(loid) oxide based respiration is not only much more prevalent in nature than is generally believed, but also is an important mode of energy generation in the habitat. Partial 16S rRNA gene sequencing revealed the bacterial community to be rich and highly diverse, containing many potentially new species. Furthermore, it appears that the worms not only possess a close symbiotic relationship with chemolithotrophic sulfide-oxidizing bacteria, but also with the metal(loid) oxide transformers. Possibly they protect the worms through reduction of the toxic compounds that would otherwise be harmful to the host.

Draft Genome Sequence of a Potential Nitrate-Dependent Fe(II)-Oxidizing Bacterium, Aquabacterium parvum B6

Aquabacterium parvum B6 is a potential nitrate-dependent Fe(II)-oxidizing bacterium. The genes related to its denitrifying mechanism and iron metabolisms were unknown. We present the draft genome of Aquabacterium parvum B6, which could provide further insight into the nitrate-dependent Fe(II)-oxidizing mechanism of strain B6.