Comparative Analysis of Denitrifying Activities of Hyphomicrobium nitrativorans, Hyphomicrobium denitrificans, and Hyphomicrobium zavarzinii

Metabolic coupling of aerobic methane oxidation and short-cut nitrification and denitrification for anaerobic effluent treatment in photo-sequencing batch biofilm reactor

This study explored the use of algae to supply oxygen in situ as an alternative to mechanical aeration for anaerobic effluent treatment in a photo-sequencing batch biofilm reactor (PSBBR). By establishing alternating aerobic (dissolved oxygen (DO) > 2 mg /L)/anoxic conditions (<0.5 mg-DO/L) through a 6-h off/6-h on biogas sparging cycle and continuous illumination (1500-3000 lux), the PSBBR achieved a significant ammonia removal rate of 15-25 mg N L-1d-1. This system demonstrated robust partial nitrification and nitrite reduction activities, coupled with aerobic methane oxidation. Metagenomic analysis revealed the enrichment of key microbial groups, including Leptolyngbyaceae, Methylocystis, Nitrosomonas and Hyphomicrobium. The key functional genes of methane (mmo, mdh, gfa, frm and fdh) and nitrogen (amo, hao, narGHI, and napAB) metabolisms were identified, while notably lacking nitrite oxidation genes. In conclusion, this study provides a promising post-treatment approach for anaerobic effluent through integrating biogas utilization with efficient nitrogen removal.

Development of a microbiome for phenolic metabolism based on a domestication approach from lab to industrial application

Despite a lot of efforts devoted to construct efficient microbiomes, there are still major obstacles to moving from the lab to industrial applications due to the inapplicability of existing technologies or limited understanding of microbiome variation regularity. Here we show a domestication strategy to cultivate an effciient and resilient functional microbiome for addressing phenolic wastewater challenges, which involves directional domestication in shaker, laboratory water test in small-scale, gas test in pilot scale, water test in pilot scale, and engineering application in industrial scale. The domestication process includes the transition from water to gas, which provided complex transient environment for screening of a more adaptable and robust microbiome, thereby mitigating the performance disparities encountered when transitioning from laboratory experimentation to industrial engineering applications. Within the domestication and application processes for treating phenolic resin wastewater, a powerful functional microbiome was built by self-assembly. This leads to an augmented biodiversity and the development of more intricate phenol and formaldehyde metabolic pathways. The incorporation of increased stochastic processes and random network characteristics further suggested the stability of the microbial community during the application phase. This study elucidates the self-assembly process of microbial communities during the artificial construction process, showcasing their adaptive evolution under different adverse conditions. It serves as a noteworthy case study for the artificial construction of a microbiome for the engineering application of treating industrial wastewater.

Outstanding enrichment of ladderane lipids in anammox bacteria: Overlooked effect of pH

Ladderane lipids synthesised by anammox bacteria hold significant potential for applications in jet fuel, drug delivery, and optoelectronics. Despite the widespread use of anammox bacteria in nitrogen removal from wastewater, the optimal conditions for maximising ladderane production remain unclear, limiting their broader application. To address this, we operated a fed-batch bioreactor with anammox bacteria, gradually adjusting the pH from 6.5 to 7.5 while regularly sampling for microbial community composition (Illumina sequencing), proteins, and ladderane lipids (UHPLC-HRMS). Our findings reveal that ladderane production positively correlates with rising pH increasing nearly fivefold as pH rose from 6.5 to 7.5, with a notable shift towards lipids containing two ladderane alkyl chains at higher pH. However, the conditions at an alkaline pH range also induced mild stress in anammox bacteria, as evidenced by our proteomic and microbial community data. Therefore, we propose maintaining a pH above 7.5 to enrich ladderane-rich anammox biomass but emphasise the need for gradual adaptation. This approach could optimise anammox installations for producing high-value ladderane lipids from wastewater.

Underground fires shape the structure of microbial communities and select for thermophilic bacteria through a temperature gradient

A detailed diversity analysis of the prokaryotic and fungal communities in soil impacted by an underground fire located in the Trans-Mexican volcanic belt, Mexico, is described. Microbial diversity data obtained from soils at different depths and temperatures (27 °C, 42 °C, 50 ºC and 54 ºC) were analyzed, and Firmicutes increased in abundance as the temperature augmented, and Proteobacteria mainly decreased in abundance at high temperatures compared to unaffected soils. The fungal phylum Ascomycota was the most abundant, with no significant changes. A clear reduction in the richness of both prokaryotic and eukaryotic operational taxonomic units (OTUs) was observed in the affected soils. At the genus level, Bacillus species were the most abundant among bacteria, while Aspergillus, Penicillium, and Mortierella were dominant fungal genera at higher temperatures. Interestingly, the physicochemical parameters of the affected soils modified organic matter, which was indirectly correlated with the presence of some microbial taxa. Likewise, we obtained 308 soil bacterial isolates from both control and affected soils. Among these, the taxa from the phyla Actinobacteria and Firmicutes demonstrated the highest thermotolerance in the affected soils. Our findings shed light on the impact of underground fires on the structure of microbial communities, favoring an abundance of thermotolerant microbes.

YeeE-like bacterial SoxT proteins mediate sulfur import for oxidation and signal transduction

Many sulfur-oxidizing prokaryotes oxidize sulfur compounds through a combination of initial extracytoplasmic and downstream cytoplasmic reactions. Facultative sulfur oxidizers adjust transcription to sulfur availability. While sulfur-oxidizing enzymes and transcriptional repressors have been extensively studied, sulfur import into the cytoplasm and how regulators sense external sulfur are poorly understood. Addressing this gap, we show that SoxT1A and SoxT1B, which resemble YeeE/YedE-family thiosulfate transporters and are encoded alongside sulfur oxidation and transcriptional regulation genes, fulfill these roles in the Alphaproteobacterium Hyphomicrobium denitrificans. SoxT1A mutants are sulfur oxidation-negative despite high transcription levels of sulfur oxidation genes, showing that SoxT1A delivers sulfur to the cytoplasm for its further oxidation. SoxT1B serves as a signal transduction unit for the transcriptional repressor SoxR, as SoxT1B mutants are sulfur oxidation-negative due to low transcription unless SoxR is also absent. Thus, SoxT1A and SoxT1B play essential but distinct roles in oxidative sulfur metabolism and its regulation.

Methane-oxidizing bacterial community dynamics in sub-alpine forest soil

Microbial activities in sub-alpine forest soil influence global cycling of the potent greenhouse gas methane. Understanding the dynamics of methane-oxidizing bacterial communities, particularly the roles of potentially active versus total microbial populations, is necessary for reducing uncertainty in global methane budget estimates. However, our understanding of the factors influencing methane cycling in forest soils is limited by our lack of knowledge about the biology of the microbes involved and how these communities are shaped by their environment. Here, we compared the composition and potential activity of microbial communities using 16S rRNA gene amplicon sequencing of total genomic DNA (gDNA) and potentially active complementary DNA (cDNA) from shallow soil in Red Butte Canyon (Salt Lake City, Utah, USA). We compared riparian and upland soils at two time points in the growing season and found distinct differences in both the community composition of the gDNA and cDNA libraries and the potential drivers of these community structures. Aerobic methane-oxidizing bacteria (methanotrophs) were detected in all samples, with cDNA libraries containing a higher average relative abundance and diversity of methanotrophs compared to gDNA libraries. Methane flux at the sample sites did not significantly correlate to the relative abundance (gDNA) or potential activity (cDNA) of methanotrophs. In the cDNA libraries, there were significant positive correlations between the abundance of Methylococcaceae family methanotrophs and several non-methanotrophic methylotrophs previously found to be associated with methane-oxidizing bacterial communities. These findings suggest a complex relationship between methane-cycling bacterial communities and methane flux and highlight the need for further in situ studies to understand the environmental and ecological influences of these microbial consortia.

IMPORTANCE

Methane-oxidizing bacteria are found in diverse soil and sediment environments and play an important role in mitigating flux of this potent greenhouse gas into the atmosphere. However, it is unclear how these bacteria and their associated communities are structured in the environment and how their activity ultimately influences methane flux. In this work, we examine the composition and structure of methane-oxidizing bacterial communities in sub-alpine forest soil and find soil- and time-specific differences between the stable and potentially active populations. We also find that the potentially active populations of certain methanotrophs and non-methanotrophs are positively correlated. This work provides a step toward refining our understanding of microbially mediated biogeochemical cycles.

Assessing the impact of soil microbial fuel cells on atrazine removal in soil

Widespread pesticide use in agriculture is a major source of soil pollution, driving biodiversity loss and posing serious threads to human health. The recalcitrant nature of most of these pesticides demands for effective remediation strategies. In this study, we assess the ability of soil microbial fuel cell (SMFC) technology to bioremediate soil polluted by the model pesticide atrazine. To elucidate the degradation mechanism and consequently define effective implementation strategies, we provide the first comprehensive investigation of the SMFC performance, in which the monitoring of the electrochemical performance of the system is combined with Quadrupole Time-of-Flight (QTOF) mass spectrometry and microbial analyses. Our results show that, while both SMFC and natural attenuation lead to a reduction on atrazine levels, the SMFC modulates the activity of different microbial pathways. As a result, atrazine degradation by natural attenuation leads to high levels of deisoproylatrazine (DIPA), a very toxic degradation metabolite, while DIPA levels in soil treated by SMFC remain comparatively low. The beta diversity and differential abundance analyses revealed how the microbial community evolves over time in the SMFCs degrading atrazine, demonstrating the enrichment of electroactive taxa on the anode, and the enrichment of a mixture of electroactive and atrazine-degrading taxa at the cathode. The detection and taxonomic classification of peripheral atrazine degrading genes, atzA, atzB and atzC, was carried out in combination with the differential abundance analysis. Results revealed that these genes are likely harboured by members of the order Rhizobiales enriched at the cathode, thus promoting atrazine degradation via the conversion of hydroxyatrazine (HA) into N-isopropylammelide (NIPA), as confirmed by mass spectrometry data. Overall, the comprehensive approach adopted in this work, provides fundamental insights into the degradation pathways of atrazine in soil by SMFC technology, which is critical for practical applications, thus suggesting an effective approach to advance research in the field.

Organophosphorus mineralizing-Streptomyces species underpins uranate immobilization and phosphorus availability in uranium tailings

Phosphate-solubilizing bacteria (PSB) are important but often overlooked regulators of uranium (U) cycling in soil. However, the impact of PSB on uranate fixation coupled with the decomposition of recalcitrant phosphorus (P) in mining land remains poorly understood. Here, we combined gene amplicon sequencing, metagenome and metatranscriptome sequencing analysis and strain isolation to explore the effects of PSB on the stabilization of uranate and P availability in U mining areas. We found that the content of available phosphorus (AP), carbonate-U and Fe-Mn-U oxides in tailings was significantly (P < 0.05) higher than their adjacent soils. Also, organic phosphate mineralizing (PhoD) bacteria (e.g., Streptomyces) and inorganic phosphate solubilizing (gcd) bacteria (e.g., Rhodococcus) were enriched in tailings and soils, but only organic phosphate mineralizing-bacteria substantially contributed to the AP. Notably, most genes involved in organophosphorus mineralization and uranate resistance were widely present in tailings rather than soil. Comparative genomics analyses supported that organophosphorus mineralizing-Streptomyces species could increase soil AP content and immobilize U(VI) through organophosphorus mineralization (e.g., PhoD, ugpBAEC) and U resistance related genes (e.g., petA). We further demonstrated that the isolated Streptomyces sp. PSBY1 could enhance the U(VI) immobilization mediated by the NADH-dependent ubiquinol-cytochrome c reductase (petA) through decomposing organophosphorous compounds. This study advances our understanding of the roles of PSB in regulating the fixation of uranate and P availability in U tailings.

The potential of ferrihydrite-synthetic humic-like acid composite as a soil amendment for metal-contaminated agricultural soil: Immobilization mechanisms by combining abiotic and biotic perspectives

In-situ passivation technique has attracted increasing attention for metal-contaminated agricultural soil remediation. However, metal immobilization mechanisms are mostly illustrated based on metal speciation changes and alterations in soil physicochemical properties from a macroscopic and abiotic perspective. In this study, a ferrihydrite-synthetic humic-like acid composite (FH-SHLA) was fabricated and applied as a passivator for a 90-day soil incubation. The heavy metals immobilization mechanisms of FH-SHLA were investigated by combining both abiotic and biotic perspectives. Effects of FH-SHLA application on soil micro-ecology were also evaluated. The results showed that the 5%FH-SHLA treatment significantly decreased the DTPA-extractable Pb, Cd and Zn by 80.75%, 46.82% and 63.63% after 90 days of incubation (P < 0.05), respectively. Besides, 5% FH-SHLA addition significantly increased soil pH, soil organic matter content and cation exchange capacity (P < 0.05). The SEM, FTIR, and XPS characterizations revealed that the abiotic metal immobilization mechanisms by FH-SHLA included surface complexation, precipitation, electrostatic attraction, and cation-π interactions. For biotic perspective, in-situ microorganisms synergistically participated in the immobilization process via sulfide precipitation and Fe mineral production. FH-SHLA significantly altered the diversity and composition of the soil microbial community, and enhanced the intensity and complexity of the microbial co-occurrence network. Both metal bioavailability and soil physiochemical parameters played a vital role in shaping microbial communities, while the former contributed more. Overall, this study provides new insight into the heavy metal passivation mechanism and demonstrates that FH-SHLA is a promising and environmentally friendly amendment for metal-contaminated soil remediation.

Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss

Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d-1 and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d-1, respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.

Distinctive biotransformation and biodefluorination of 6:2 versus 5:3 fluorotelomer carboxylic acids by municipal activated sludge

Fluorotelomer carboxylic acids (FTCAs) represent an important group of per- and polyfluoroalkyl substances (PFAS) given their high toxicity, bioaccumulation potential, and frequent detection in landfill leachates and PFAS-impacted sites. In this study, we assessed the biodegradability of 6:2 FTCA and 5:3 FTCA by activated sludges from four municipal wastewater treatment plants (WWTPs) in the New York Metropolitan area. Coupling with 6:2 FTCA removal, significant fluoride release (0.56∼1.83 F-/molecule) was evident in sludge treatments during 7 days of incubation. Less-fluorinated transformation products (TPs) were formed, including 6:2 fluorotelomer unsaturated carboxylic acid (6:2 FTUCA), perfluorohexanoic acid (PFHxA), perfluoropentanoic acid (PFPeA), and perfluorobutanoic acid (PFBA). In contrast, little fluoride (0.01∼0.09 F-/molecule) was detected in 5:3 FTCA-dosed microcosms, though 25∼68% of initially dosed 5:3 FTCA was biologically removed. This implies the dominance of "non-fluoride-releasing pathways" that may contribute to the formation of CoA adducts or other conjugates over 5:3 FTCA biotransformation. The discovery of defluorinated 5:3 FTUCA revealed the possibility of microbial attacks of the C-F bond at the γ carbon to initiate the transformation. Microbial community analysis revealed the possible involvement of 9 genera, such as Hyphomicrobium and Dechloromonas, in aerobic FTCA biotransformation. This study unraveled that biotransformation pathways of 6:2 and 5:3 FTCAs can be divergent, resulting in biodefluorination at distinctive degrees. Further research is underscored to uncover the nontarget TPs and investigate the involved biotransformation and biodefluorination mechanisms and molecular basis.

Distribution of mercury in modern bottom sediments of the Beaufort Sea in relation to the processes of early diagenesis: Microbiological aspect

This study investigated the contents of total mercury (THg), trace metals, and CH4 and determined the signature microbes involved in various biogeochemical processes in the sediment of the Canadian Beaufort Sea. The THg ranged between 32 and 63 μg/kg and the trace metals such as Fe, Al, Mn, and Zn were significant in distributions. The pH, SO42-, Fe2+, and redox proxy metals were crucial factors in the spatial and vertical heterogeneity of geochemical distributions. CH4 was detected only at the mud volcano site. Microbial analyses identified Clostridium, Desulfosporosinus, Desulfofustis, and Desulftiglans as the predominant Hg methylators and sulfate reducers; Nitrosopumilus and Hyphomicrobium as the major nitrifiers and denitrifiers; Methanosarcina and Methanosaeta as keystone methanogens; and Methyloceanibacter and Methyloprofundus as signature methanotrophs. Altogether, this study expands the current understanding of the microbiological and geochemical features and could be helpful in predicting ecosystem functions in the Canadian Beaufort Sea.

Rapid start-up strategy and microbial population evolution of anaerobic ammonia oxidation biofilm process for low-strength wastewater treatment

The implementation of the anaerobic ammonium oxidation (anammox) process in treating low-strength wastewater is limited by the difficulty in enriching anammox bacteria (AnAOB). Here, the first enrichment of AnAOB at a high nitrogen (N) loading rate (NLR) as a strategy was proposed to achieve the rapid start-up of the anammox biofilm process treating low-strength wastewater. The long-term stability of the anammox biofilm process after start-up operating at a low NLR of 0.2-0.4 kg N/(m3⋅d) was evaluated. Results showed that the N removal efficiency was up to 75 % under a low NLR of 0.2 kg N/(m3⋅d) condition. Low-strength organic matter promoted the metabolic coupling between partial denitrifying bacteria (PDB) and AnAOB. The genus Candidatus Brocadia as AnAOB (18 %-27 %) can coexist with Limnobacter (PDB, 9 %-12 %) for efficient N removal. This study offers a rapid start-up strategy of anammox biofilm process in treating low-strength wastewater.

Incubation study on remediation of nitrate-contaminated soil by Chroococcus sp

The possibility of using the non-nitrogen-fixing cyanobacterium (Chroococcus sp.) for the reduction of soil nitrate contamination was tested through Petri dish experiments. The application of 0.03, 0.05 and 0.08 mg/cm2 Chroococcus sp. efficiently removed NO3--N from the soil through assimilation of nitrate nutrient and promotion of soil denitrification. At the optimal application dose of 0.05 mg/cm2, 44.06%, 36.89% and 36.17% of NO3--N were removed at initial NO3--N concentrations of 60, 90 and 120 mg/kg, respectively. The polysaccharides released by Chroococcus sp. acted as carbon sources for bacterial denitrification and facilitated the reduction of soil salinity, which significantly (p < 0.05) stimulated the growth of denitrifying bacteria (Hyphomicrobium denitrificans and Hyphomicrobium sp.) as well as significantly (p < 0.05) elevated the activities of nitrate reductase and nitrite reductase by 1.07-1.23 and 1.15-1.22 times, respectively. The application of Chroococcus sp. promoted the dominance of Nocardioides maradonensis in soil microbial community, which resulted in elevated phosphatase activity and increased available phosphorus content. The application of Chroococcus sp. positively regulated the growth of soil bacteria belonging to the genera Chitinophaga, Prevotella and Tumebacillus, which may contribute to increased soil fertility through the production of beneficial enzymes such as invertase, urease and catalase. To date, this is the first study verifying the remediation effect of non-nitrogen-fixing cyanobacteria on nitrate-contaminated soil.

Nature-Based Solution to Eliminate Cyanotoxins in Water Using Biologically Enhanced Biochar

Climate change and high eutrophication levels of freshwater sources are increasing the occurrence and intensity of toxic cyanobacterial blooms in drinking water supplies. Conventional water treatment struggles to eliminate cyanobacteria/cyanotoxins, and expensive tertiary treatments are needed. To address this, we have designed a sustainable, nature-based solution using biochar derived from waste coconut shells. This biochar provides a low-cost porous support for immobilizing microbial communities, forming biologically enhanced biochar (BEB). Highly toxic microcystin-LR (MC-LR) was used to influence microbial colonization of the biochar by the natural lake-water microbiome. Over 11 months, BEBs were exposed to microcystins, cyanobacterial extracts, and live cyanobacterial cells, always resulting in rapid elimination of toxins and even a 1.6-1.9 log reduction in cyanobacterial cell numbers. After 48 h of incubation with our BEBs, the MC-LR concentrations dropped below the detection limit of 0.1 ng/mL. The accelerated degradation of cyanotoxins was attributed to enhanced species diversity and microcystin-degrading microbes colonizing the biochar. To ensure scalability, we evaluated BEBs produced through batch-scale and continuous-scale pyrolysis, while also guaranteeing safety by maintaining toxic impurities in biochar within acceptable limits and monitoring degradation byproducts. This study serves as a proof-of-concept for a sustainable, scalable, and safe nature-based solution for combating toxic algal blooms.

Ecological mechanisms of biofilm development in the hybrid sludge-biofilm process: Implications for process start-up and optimization

The hybrid sludge-biofilm processes have been widely applied for the construction or upgradation of biological wastewater treatment process. Ecological mechanisms of biofilm development remain unclear in the hybrid ecosystem, because of the intricate interactive effects between sludge and biofilms. Herein, the establishment principles of biofilms with distinct coexisting sludge amounts were uncovered by varying sludge retention times (SRTs) from 5 to 40 days in the hybrid process. With the increasing of SRTs, biofilm biomass decreased with the increase of suspended sludge, resulting in lower biofilm proportion. As estimated by the Gompertz growth model, the increased sludge amounts (i.e., higher SRTs of 20 and 40 days) prolonged the initial colonization stage and decreased the specific development rate of biofilms when compared to lower sludge amounts with the shorter SRTs (i.e., 5 and 10 days). Null model analysis demonstrated that deterministic homogenous selection could facilitate the colonization and accumulation of biofilms with less coexisting sludge (SRT of 10 days). However, stochastic ecological drift and homogenizing dispersal dominated the colonization and accumulation stages of biofilms with more coexisting sludge (SRT of 20 days), respectively. The ecological networks reflected that positively-related taxa presented taxonomic relatedness, whereas high inconsistency of taxonomic relatedness was observed among aggregate forms or development stages as affected by varied SRTs. The high incidence of intra-taxa co-occurrence patterns suggested that taxa with similar ecological niches could be specifically selected in biofilms when being exposed with less coexisting sludge. This study uncovered ecological mechanisms of biofilm development driven by varying the SRTs of suspended sludge, which would help to propose appropriate strategies for the efficient start-up and optimization of the hybrid sludge-biofilm system.

The existence of ferric hydroxide links the carbon and nitrogen cycles by promoting nitrite-coupled methane anaerobic oxidation

Microorganism-mediated anaerobic oxidation of methane can efficiently mitigate methane atmospheric emissions and is a key process linking the biogeochemical cycles of carbon, nitrogen, and iron. The results showed that methane oxidation and nitrite removal rates in the CF were 1.12 and 1.28 times higher than those in CK, respectively, suggesting that ferric hydroxide can enhance nitrite-driven AOM. The biochemical process was mediated by the enrichment of methanogens, methanotrophs, and denitrifiers. Methanobacterium and Methanosarcina were positively correlated with Fe3+ and Fe2+, whereas Methylocystis and Methylocaldum were positively correlated with methane, and denitrifiers were positively correlated with nitrite. Metagenomic analysis revealed that the genes related to methane oxidation, nitrogen reduction, and heme c-type cytochrome were upregulated in CF, indicating that a synergistic action of bacteria and methanogens drove AOM via diverse metabolic pathways, within which ferric hydroxide played a crucial role. This study provides novel insights into the synergistic mechanism of ferric iron and nitrite-driven AOM.

In the Alphaproteobacterium Hyphomicrobium denitrificans SoxR Serves a Sulfane Sulfur-Responsive Repressor of Sulfur Oxidation

In organisms that use reduced sulfur compounds as alternative or additional electron donors to organic compounds, transcriptional regulation of genes for enzymes involved in sulfur oxidation is needed to adjust metabolic flux to environmental conditions. However, little is known about the sensing and response to inorganic sulfur compounds such as thiosulfate in sulfur-oxidizing bacteria. In the Alphaproteobacterium Hyphomicrobium denitrificans, one strategy is the use of the ArsR-SmtB-type transcriptional regulator SoxR. We show that this homodimeric repressor senses sulfane sulfur and that it is crucial for the expression not only of sox genes encoding the components of a truncated periplasmic thiosulfate-oxidizing enzyme system but also of several other sets of genes for enzymes of sulfur oxidation. DNA binding and transcriptional regulatory activity of SoxR are controlled by polysulfide-dependent cysteine modification. The repressor uses the formation of a sulfur bridge between two conserved cysteines as a trigger to bind and release DNA and can also form a vicinal disulfide bond to orchestrate a response to oxidizing conditions. The importance of the sulfur bridge forming cysteines was confirmed by site-directed mutagenesis, mass spectrometry, and gel shift assays. In vivo, SoxR interacts directly or indirectly with a second closely related repressor, sHdrR.

Characteristics and comparisons of the aerobic and anaerobic denitrification of a Klebsiella oxytoca strain: Performance, electron transfer pathway, and mechanism

The performance and electron (e^-) transfer mechanisms of anaerobic and aerobic denitrification by strain Klebsiella were investigated in this study. The RT-PCR results demonstrated that the membrane bound nitrate reductase gene (narG) and Cu-nitrite reductase gene (nirK) were responsible for both aerobic and anerobic denitrification. The extreme low gene relative abundance of nirK might be responsible for the severe accumulation of NO₂^--N (nitrogen in the form of NO₂^- ion) under anaerobic condition. Moreover, the nitrite reductase (Nir) activity was 0.31 μg NO₂^--N min^-1 mg^-1 protein under anaerobic conditions, which was lower than that under aerobic conditions (0.38 μg NO₂^--N min^-1 mg^-1 protein). By using respiration chain inhibitors, the e^- transfer pathways of anaerobic and aerobic denitrification of Klebsiella strain were constructed. Fe-S protein and Complex III were the core components under anaerobic conditions, while Coenzyme Q (CoQ), Complexes I and III played a key role in aerobic denitrification. Nitrogen assimilation was found to be the main way to generate NH₄⁺-N (nitrogen in the form of NH₄⁺ ion) during anaerobic denitrification, and also served as the primary nitrogen removal way under aerobic condition. The results of this study may help to improve the understanding of the core components of strain Klebsiella during aerobic and anaerobic denitrifications, and may suggest potential applications of the strain for nitrogen-containing wastewater.

The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis

The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.

Microbial community structure and denitrification responses to cascade low-head dams and their contribution to eutrophication in urban rivers

Low-head dams are one of the most common hydraulic facilities, yet they often fragment rivers, leading to profound changes in aquatic biodiversity and river eutrophication levels. Systematic assessments of river ecosystem structure and functions, and their contribution to eutrophication, are however lacking, especially for urban rivers where low-head dams prevail. In this study, we address this gap with a field survey on microbial community structure and ecosystem function, in combination with hydrological, environmental and ecological factors. Our findings revealed that microbial communities showed significant differences among the cascade impoundments, which may be due to the environment heterogeneity resulting from the cascade low-head dams. The alternating lentic-lotic flow environment created by the low-head dams caused nutrient accumulation in the cascade impoundments, enhancing environmental sorting and interspecific competition relationships, and thus possibly contributing to the reduction in sediment denitrification function. Decreased denitrification led to excessive accumulation of nutrients, which may have aggravated river eutrophication. In addition, structural equation model analysis showed that flow velocity may be the key controlling factor for river eutrophication. Therefore, in the construction of river flood control and water storage systems, the location, type and water storage capacity of low-head dams should be fully considered to optimize the hydrodynamic conditions of rivers. To summarize, our findings revealed the cumulative effects of cascade low-head dams in an urban river, and provided new insights into the trade-off between construction and decommissioning of low-head dams in urban river systems.

Biotrickling Filtration for the Reduction of N2O Emitted during Wastewater Treatment: Results from a Long-Term In Situ Pilot-Scale Testing

Wastewater treatment plants (WWTPs) are a major source of N₂O, a potent greenhouse gas with 300 times higher global warming potential than CO₂. Several approaches have been proposed for mitigation of N₂O emissions from WWTPs and have shown promising yet only site-specific results. Here, self-sustaining biotrickling filtration, an end-of-the-pipe treatment technology, was tested in situ at a full-scale WWTP under realistic operational conditions. Temporally varying untreated wastewater was used as trickling medium, and no temperature control was applied. The off-gas from the covered WWTP aerated section was conveyed through the pilot-scale reactor, and an average removal efficiency of 57.9 ± 29.1% was achieved during 165 days of operation despite the generally low and largely fluctuating influent N₂O concentrations (ranging between 4.8 and 96.4 ppmv). For the following 60-day period, the continuously operated reactor system removed 43.0 ± 21.2% of the periodically augmented N₂O, exhibiting elimination capacities as high as 5.25 g N₂O m^-3·h^-1. Additionally, the bench-scale experiments performed abreast corroborated the resilience of the system to short-term N₂O starvations. Our results corroborate the feasibility of biotrickling filtration for mitigating N₂O emitted from WWTPs and demonstrate its robustness toward suboptimal field operating conditions and N₂O starvation, as also supported by analyses of the microbial compositions and nosZ gene profiles.

Groundwater Microbiology of an Urban Open-Loop Ground Source Heat Pump with High Methane

Ground source heat pumps (GSHPs) are low-carbon alternatives to gas boilers for decarbonizing heating. Open-loop GSHP systems abstract groundwater, pass it through a heat exchanger, and return it to ground or surface water. Groundwater samples from the top and base of an abstraction and a recharge borehole of an open-loop GSHP system in Cardiff, UK were assessed, and compared to two local boreholes in the same aquifer. Groundwater samples were taken when the GSHP system was active (once) and inactive (twice) and analyzed for changes in geochemistry, viable cell counts, and microbial community (16S rRNA gene sequencing). The GSHP had a distinct geochemistry and microbial community compared to the control boreholes, and the abstraction borehole showed greater variability than the recharge borehole. The microbial community of the GSHP system showed an increase in relative abundance of genera involved in oxidation of methane and methylated compounds, of which Methylotenera was the most abundant (up to 83.9% of 16S rRNA gene sequences). There were also changes in genera associated with nitrification (Nitrospira, Nitrosomonas) and those with potential for sulfur and iron cycling (Rhodoferax). Methane concentration was analyzed after identification of methylotrophs and found that methane concentrations were up to 2855 μg L^-1 , thus likely having had a significant impact on the bacterial communities present. Understanding the microbiology and biogeochemistry of GSHP systems provides insight into potential issues with local infrastructure and long-term system performance, and supports modeling to maximize efficient and sustainable use of the subsurface.

Effects of multiple key factors on the performance of petroleum coke-based constructed wetland-microbial fuel cell

In this study, two constructed wetland-microbial fuel cells (CW-MFC), including a closed-circuit system (CCW-MFC) and an open-circuit system (OCW-MFC) with petroleum coke as electrode and substrate, were constructed to explore the effect of multiple key factors on their operation performances. Compared to a traditional CW, the CCW-MFC system showed better performance, achieving an average removal efficiency of COD, NH₄⁺-N, and TN of 94.49 ± 1.81%, 94.99 ± 4.81%, and 84.67 ± 5.6%, respectively, when the aeration rate, COD concentration, and hydraulic retention time were 0.4 L/min, 300 mg/L, and 3 days. The maximum output voltage (425.2 mV) of the CCW-MFC system was achieved when the aeration rate was 0.2 L/min. In addition, the CCW-MFC system showed a greater denitrification ability due to the higher abundance of Thiothrix that might attract other denitrifying bacteria, such as Methylotenera and Hyphomicrobium, to participate in the denitrifying process, indicating the quorum sensing could be stimulated within the denitrifying microbial community.

Quorum sensing responses of r-/K-strategists Nitrospira in continuous flow and sequencing batch nitrifying biofilm reactors

A better understanding of r-/K-strategists nitrifiers will help to balance the design and operation of bioprocesses for efficient pollution removal from wastewater. The objectives of study were to investigate the nitrite oxidation biokinetics, biofilm property, microbial community and quorum sensing (QS) of nitrifying biofilm in a continuously flow reactor (CFR) and a sequencing batch reactor (SBR). Results showed that nitrite-oxidizing bacteria were estimated to have a nitrite half saturation constant of 76.23 and 224.73 μM in CFR and SBR, respectively. High-throughput and metagenomic sequencing results showed that Nitrospira and Candidatus Nitrospira defluvii were the dominated nitrite-oxidizing taxa performing nitrite oxidation in both reactors. Nitrifying biofilm developed in CFR and SBR showed obviously different properties. Biofilm in SBR had an obviously higher ratio of polysaccharide and protein in extracellular polymeric substances, and higher thickness than in CFR. Metagenomics and chemical analysis revealed various types of acyl-homoserine lactone (AHL) circuit genes (e.g., luxI, lasI, hdtS) and four types of AHL signaling substances (e.g., C₆-HSL, C₈-HSL, C₁₀-HSL and 3-oxo-C₁₀-HSL) in nitrifying biofilm. The concentrations of these AHLs in biomass and water phases were obviously higher in SBR than that in CFR. Together, AHLs-based QS might affect the formation of nitrifying biofilm and thus contribute to the different biokinetics of Nitrospira in CFR and SBR. Our insights may reveal the molecular mechanism of Nitrospira for different biokinetics, and indicate the AHL association with Nitrospira adaptation to various conditions.

Adaptive evolutionary strategy coupled with an optimized biosynthesis process for the efficient production of pyrroloquinoline quinone from methanol

BACKGROUND

Pyrroloquinoline quinone (PQQ), a cofactor for bacterial dehydrogenases, is associated with biological processes such as mitochondriogenesis, reproduction, growth, and aging. Due to the extremely high cost of chemical synthesis and low yield of microbial synthesis, the election of effective strains and the development of dynamic fermentation strategies for enhancing PQQ production are meaningful movements to meet the large-scale industrial requirements.

RESULTS

A high-titer PQQ-producing mutant strain, Hyphomicrobium denitrificans FJNU-A26, was obtained by integrating ARTP (atmospheric and room‑temperature plasma) mutagenesis, adaptive laboratory evolution and high-throughput screening strategies. Afterward, the systematic optimization of the fermentation medium was conducted using a one-factor-at-a-time strategy and response surface methodology to increase the PQQ concentration from 1.02 to 1.37 g/L. The transcriptional analysis using qRT-PCR revealed that the expression of genes involved in PQQ biosynthesis were significantly upregulated when the ARTP-ALE-derived mutant was applied. Furthermore, a novel two-stage pH control strategy was introduced to address the inconsistent effects of the pH value on cell growth and PQQ production. These combined strategies led to a 148% increase in the PQQ concentration compared with that of the initial strain FJNU-6, reaching 1.52 g/L with a yield of 40.3 mg/g DCW after 144 h of fed-batch fermentation in a 5-L fermenter.

CONCLUSION

The characteristics above suggest that FJNU-A26 represents an effective candidate as an industrial PQQ producer, and the integrated strategies can be readily extended to other microorganisms for the large-scale production of PQQ.

A metabolic puzzle: Consumption of C1 compounds and thiosulfate in Hyphomicrobium denitrificans XT

Many obligately heterotrophic methylotrophs oxidize thiosulfate as an additional electron source during growth on C₁ compounds. Although two different pathways of thiosulfate oxidation are implemented in Hyphomicrobium denitrificans X^T, a pronounced negative effect on growth rate is observed when it is cultured in the simultaneous presence of methanol and thiosulfate. In this model organism, periplasmic thiosulfate dehydrogenase TsdA catalyzes formation of the dead-end product tetrathionate. By reverse genetics we verified the second pathway that also starts in the periplasm where SoxXA catalyzes the oxidative fusion of thiosulfate to SoxYZ, from which sulfate is released by SoxB. Sulfane sulfur is then further oxidized in the cytoplasm by the sulfur-oxidizing heterodisulfide reductase-like system (sHdr) which is produced constitutively in a strain lacking the transcriptional repressor sHdrR. When exposed to thiosulfate, the ΔshdrR strain exhibited a strongly reduced growth rate even without thiosulfate in the pre-cultures. When grown on methanol, cells exhibit significantly increased NAD⁺/NADH ratios in the presence of thiosulfate. In contrast, thiosulfate did not exert any negative effect on growth rate or increase NAD⁺ levels during growth on formate. On both C₁ substrates, excretion of up to 0.5 mM sulfite as an intermediate of thiosulfate (2 mM) oxidation was recorded. Sulfite is known to form adducts with pyrroloquinoline quinone, the cofactor of periplasmic methanol dehydrogenase. We rationalize that this causes specific inhibition of methanol degradation in the presence of thiosulfate while formate metabolism in the cytoplasm remains unaffected.

Dissolved organic nitrogen derived from wastewater denitrification: Composition and nitrogenous disinfection byproduct formation

Microbially derived dissolved organic nitrogen (mDON) is a major fraction of effluent total nitrogen at wastewater treatment plants with enhanced nutrient removal, which stimulates phytoplankton blooms and formation of toxic nitrogenous disinfection by-products (N-DBPs). This study identified denitrifiers as major contributors to mDON synthesis, and further revealed the molecular composition, influential factors and synthetic microorganisms of denitrification-derived mDON compounds leading to N-DBP formation. The maximum mDON accumulated during denitrification was 8.92% of converted inorganic nitrogen, higher than that of anammox (4.24%) and nitrification (2.76%). Sodium acetate addition at relatively high C/N ratio (5-7) favored mDON formation, compared with methanol and low C/N (1-3). Different from acetate, methanol-facilitated denitrification produced 13-69% more lignin-like compounds than proteins using Orbitrap LC-MS. The most abundant N-DBPs formed from denitrification-derived mDON were N-nitrosodibutylamine and dichloroacetonitrile (13.32 μg/mg mDON and 12.21 μg/mg mDON, respectively). Major amino acids, aspartate, glycine, and alanine were positively correlated with typical N-DBPs. Biosynthesis and degradation pathways of these N-DBP precursors were enriched in denitrifiers belonging to Rhodocyclaceae, Mycobacteriaceae and Hyphomicrobiaceae. As intensive disinfection is applied at worldwide wastewater treatment plants during COVID-19, carbon source facilitated denitrification should be better managed to reduce both effluent inorganic nitrogen and DON, mitigating DON and N-DBP associated ecological risks in receiving waters.

First insights into the prokaryotic community structure of Lake Cote, Costa Rica: Influence on nutrient cycling

Prokaryotic diversity in lakes has been studied for many years mainly focusing on community structure and how the bacterial assemblages are driven by physicochemical conditions such as temperature, oxygen, and nutrients. However, little is known about how the composition and function of the prokaryotic community changes upon lake stratification. To elucidate this, we studied Lake Cote in Costa Rica determining prokaryotic diversity and community structure in conjunction with physicochemistry along vertical gradients during stratification and mixing periods. Of the parameters measured, ammonium, oxygen, and temperature, in that order, were the main determinants driving the variability in the prokaryotic community structure of the lake. Distinct stratification of Lake Cote occurred (March 2018) and the community diversity was compared to a period of complete mixing (March 2019). The microbial community analysis indicated that stratification significantly altered the bacterial composition in the epi-meta- and hypolimnion. During stratification, the Deltaproteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Euryarchaeota were dominant in the hypolimnion yet largely absent in surface layers. Among these taxa, strict or facultative anaerobic bacteria were likely contributing to the lake nitrogen biogeochemical cycling, consistent with measurements of inorganic nitrogen measurements and microbial functional abundance predictions. In general, during both sampling events, a higher abundance of Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and Cyanobacteria was found in the oxygenated layers. Lake Cote had a unique bacterial diversity, with 80% of Amplicon Sequence Variant (ASV) recovered similar to unclassified/uncultured strains and exhibits archetypal shallow lake physicochemical but not microbial fluctuations worthy of further investigation. This study provides an example of lake hydrodynamics impacts to microbial community and their function in Central American lakes with implications for other shallow, upland, and oligotrophic lake systems.

Exposure to amitriptyline induces persistent gut damages and dysbiosis of the gut microbiota in zebrafish (Danio rerio)

Amitriptyline (AMI), the most commonly prescribed tricyclic antidepressant, is widely detected in water environments. Exposure to AMI may lead to diverse adverse effects on aquatic organisms, but little is known about the effect of short-term exposure to AMI on the gut microbiota of aquatic organisms and their recovery characteristics. In the present study, adult zebrafish (Danio rerio) were exposed to AMI (0, 2.5, 10, and 40 μg/L) for seven days, and then allowed to recover in AMI-free culture water for 21 days. The exposure caused gut damages in all the AMI treated groups of zebrafish, which became more severe after recovery compared to the control group. AMI exposure also disturbed the microbiota of zebrafish guts and rearing water even after the 21-day recovery period. Furthermore, AMI exposure affected microbes involved in the substance and energy metabolic functions in zebrafish guts and tended to increase the abundance of microbial genera associated with opportunistic pathogens. In addition, the microbial predicted metabolic functions in AMI-exposed guts of zebrafish were significantly altered after the 21-day recovery period, explaining the persistent effects of short-term exposure to AMI. The results of this study suggest that acute exposure to AMI may have persistent impacts on the gut histomorphology and the gut microbiota in aquatic organisms.

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.

Reinforcement of denitrification in a biofilm electrode reactor with immobilized polypyrrole/anthraquinone-2,6-disulfonate composite cathode

In biofilm electrode reactors (BER), good nitrate removal performance can be achieved through cooperation of heterotrophic and hydrogen autotrophic denitrification under low carbon/nitrogen conditions. In this study, we proposed a more multifunctional composite cathode, which combine immobilized anthraquinone-2,6-disulphonic disodium salt (AQDS) with polypyrrole (PPy) by electrochemical polymerization-doping method. The nitrate removal performance in BER with PPy/AQDS composite cathode was obviously improved, the nitrate removal rate (4.96 mg/L·h) was almost 2.0 times higher than the control BER system, and relatively stabled nitrate removal efficiency (≥90.0%) was also achieved even as the COD/N of 2.50. Compared with the bare graphite felt, PPy/AQDS coating cathode showed much better electrocatalytic activities, which was more advantageous for in situ production of H₂ to support hydrogen autotrophic denitrification process. The PPy-bound AQDS could also act as electron intermediaries, which is beneficial to greatly promote indirect electron process between the denitrifiers and nitrate. Moreover, the PPy/AQDS composite layer formed many particles for improving the specific surface area and bio-attachment site for bacterial attachment, which was conducive for the proliferation of microorganisms and denitrification efficiency. The ratio of biofilm and electrode of PPy/AQDS biocathode was 0.32 ± 0.08, which was 2.46 times than bare electrode (0.13 ± 0.06). Furthermore, enrichment of specific denitrifiers and enhancement of denitrifying enzyme activity was obtained using PPy/AQDS treated electrode, the much higher relative abundance of Thauera of PPy/AQDS biocathode was 1.58 times to the application of bare graphite felt.

Alterations in microbial community during the remediation of a black-odorous stream by acclimated composite microorganisms

Microbial application is an efficient, economical, and ecofriendly method for remediating black-odorous rivers. In this study, the field treatment effect and microbial community changes were monitored during remediation by the acclimated complex microorganisms of a typical black-odorous stream. After the treatment, the total phosphorus and ammonia contents decreased by 74.0% and 76.3% and the concentrations of dissolved oxygen increased from 1.65 to 4.90 mg/L, indicating the effectiveness of the acclimated composite microorganisms. The proportion of Bacteroidetes decreased significantly by 48.1% and that of Firmicutes increased by 2.23% on average, and the microbial diversity index first increased and then tended to be uniform. Redundancy analysis demonstrated that the pH, dissolved oxygen, and oxidation-reduction potential together determined the composition of the microbial communities (p < 0.05). These findings showed that the acclimated composite microorganisms can effectively remediate the black odor.

Response of bacterial communities in saline-alkali soil to different pesticide stresses

The objective is to understand the diversity of bacteria-degrading pesticide pollutants in Xinjiang saline-alkali soil environment and resolve the lack of suitable degrading bacteria resources for bioremediation of pesticide pollution in this environment. The soil of long-term continuous cropping cotton fields in Xinjiang was used to culture the degrading bacterial communities under long-term stress of five pesticides, such as beta-cypermethrin. Then, the degradation rate and structural composition of each bacterial communities were analyzed. The soil bacterial diversity in Xinjiang saline-alkali cotton fields was high, from which not only imidacloprid and other commonly and once used pesticide-degrading bacterial communities were enriched but also isoprocarb-degrading bacterial communities, which had never been used, were enriched. After long-term passage, the structural composition of each degrading bacterial communities was stable, and the degradation rates were between 17 and 48%, respectively, in a specific culture period. Each degrading bacterial communities covers many reported pesticide-degrading bacterial genera and contains unique bacterial genera in each 3. These results laid a foundation for studying the metabolic pathway of pesticide pollutants in saline-alkali environment and exploring microbial resources in Xinjiang. Graphical Abstract Variety of pesticide degrading bacteria resources in saline alkali soil of Xinjiang.

Full-scale transition from denitrification to partial denitrification-anammox (PdNA) in deep-bed filters: Operational strategies for and benefits of PdNA implementation

This study shows for the first time more than 2 years of operation of a mainstream anammox application at full-scale under temperate climate. This implementation of partial denitrification-anammox (PdNA) in deep bed filters at the HRSD York River treatment plant was demonstrated to achieve the benefits of shortcut nitrogen removal without nitrite oxidizing bacteria (NOB) out-selection. The transition from denitrification to PdNA filters required bleeding ammonium to the filters using an optimized ammonium versus NOx (AvN) control in the upstream aeration tanks and maintaining a nitrate residual in the filter effluent through feedforward/feedback control. The latter actions led to savings of 85% in methanol, 100% in alkalinity, and 35% in capacity enhancement. Up to 6 mg NH₄ ⁺ -N/L with an average of 2.2 ± 0.98 mg NH₄ ⁺ -N/L was removed through the anammox pathway, which accounted for about 15% of the overall plant nitrogen removal. Anammox enrichment was confirmed by activity testing and molecular analysis. The large excess of AnAOB capacity present in the filters (5-10 times more than normal operation) resulted in stable and reliable operation through winter conditions and showed potential for further intensification. PRACTITIONER POINTS: For the first time, long-term mainstream anammox was established full-scale through PdNA implementation in deep-bed filters. PdNA implementation required upstream aeration control optimization to provide a blend of ammonium and nitrate to the filters. Efficient anammox enrichment and retention resulted in reliable PdNA performance under different seasonal and influent conditions. PdNA implementation resulted in significant methanol and alkalinity savings and upstream capacity enhancement as ammonia removal depended less on aerobic nitrification. In the event of NOB out-selection and presence of nitrite, carbon savings in PdNA polishing filters can be enhanced via partial nitritation-anammox.

Gut Microbial Composition of Pacific Salmonids Differs across Oregon River Basins and Hatchery Ancestry

The gut microbiome may represent a relatively untapped resource in the effort to manage and conserve threatened or endangered fish populations, including wild and hatchery-reared Pacific salmonids. To clarify this potential, we defined how steelhead trout gut microbiome composition varies across watersheds and as a function of ancestry. First, we measured this variation across watersheds using wild steelhead trout sampled from nine locations spanning three river basins. While gut microbial composition differs across basins, there exist bacterial clades that are ubiquitous across all populations. Correlating the phylogenetic composition of clades with geographic distance reveals 395 clades of bacteria whose ecological distribution implicates their co-diversification with steelheads. Second, we quantified how microbiome composition varies between first generation hatchery-reared steelhead and traditional hatchery-reared steelhead. Despite being subject to the same hatchery management strategies, fish bred from wild parents carry distinct microbiomes from those bred from hatchery broodstock, implicating the role of genotype on microbiome composition. Finally, we integrated all data from both studies to reveal two distinct, yet robust clusters of community composition. Collectively, our study documents for the first time how the steelhead gut microbiome varies by geography or broodstock and uncovers microbial taxa that may indicate the watershed or hatchery from which an individual was sourced.

Can a compact biological system be used for real hydraulic fracturing wastewater treatment?

Hydraulic fracturing wastewater (HFW), a byproduct of hydraulic fracturing oil extraction, contains a complex mixture of oil, aldehydes, and benzene compounds. Efficient and eco-friendly HFW treatment means are critical for the oil extraction industry, particularly in developing countries. In this study, two biological processes namely an anaerobic/anoxic/moving bed biofilm reactor (A²-MBBR) and an A²-MBBR with a microfiltration membrane (A²-MFMBBR) were established, and assessed for the real HFW treatment. Removal efficiencies of chemical oxygen demand (COD) and NH₄⁺-N were over 92% and 95%, respectively, in both processes with a hydraulic retention time of 72 h. The majority of organic compounds in both systems identified by GC-MS were degraded in the anaerobic units. In comparison, A²-MFMBBR demonstrated higher removal efficiencies for oil, total suspended solids, and complex compounds. The average relative abundances of refractory compound degrading bacteria were 43.4% and 51.6% in the A²-MBBR and A²-MFMBBR, respectively, which was consistent with the COD and oil removal, and suggested that the MBR could maintain a high diversity of microorganisms and contribute to deep recalcitrant organics degradation. This study sheds light on the potential of using a compact biological process for the real HFW treatment.

Anaerobic degradation of perfluorooctanoic acid (PFOA) in biosolids by Acidimicrobium sp. strain A6

Anaerobic incubations were performed with biosolids obtained from an industrial wastewater treatment plant (WWTP) that contained perfluorooctanoic acid (PFOA), and with per- and polyfluoroalkyl substances- (PFAS) free, laboratory-generated, biosolids that were spiked with PFOA. Biosolid slurries were incubated for 150 days as is, after augmenting with either Acidimicrobium sp. Strain A6 or ferrihydrite, or with both, Acidimicrobium sp. Strain A6 and ferrihydrite. Autoclaved controls were run in parallel. Only the biosolids augmented with both, Acidimicrobium sp. Strain A6 and ferrihydrite showed a decrease in the PFOA concentration, in excess of 50% (total, dissolved, and solid associated). Higher concentrations of PFOA in the biosolids spiked with PFOA and no previous PFAS exposure allowed to track the production of fluoride to verify PFOA defluorination. The buildup of fluoride over the incubation time was observed in these biosolid incubations spiked with PFOA. A significant increase in the concentration of perfluoroheptanoic acid (PFHpA) over the incubations of the filter cake samples from the industrial WWTP was observed, indicating the presence of a non-identified precursor in these biosolids. Results show that anaerobic incubation of PFAS contaminated biosolids, after augmentation with Fe(III) and Acidimicrobium sp. Strain A6 can result in PFAS defluorination.

Aquaculture production of hatchling Hawaiian Bobtail Squid (Euprymna scolopes) is negatively impacted by decreasing environmental microbiome diversity

Aims

The Hawaiian Bobtail Squid (Euprymna scolopes) is a model organism for investigating host–symbiont relationships. The current scientific focus is on the microbiome within E. scolopes, while very little is known about the microbiome of the tanks housing E. scolopes. We examined the hypothesis that bacterial communities and geochemistry within the squid tank environment correlate with the production of viable paralarval squid.

Methods and Results

Total DNA was extracted from sediment and filtered water samples from ‘productive’ squid cohorts with high embryonic survival and paralarval hatching, ‘unproductive’ cohorts with low embryonic survival and paralarval hatching. As a control total DNA was extracted from environmental marine locations where E. scolopes is indigenous. Comparative analysis of the bacterial communities by the 16S rRNA gene was performed using next generation sequencing. Thirty‐eight differentially abundant genera were identified in the adult tank waters. The majority of the sequences represented unclassified, candidate or novel genera. The characterized genera included Aquicella, Woeseia and Ferruginibacter, with Hyphomicrobium and Rhizohapis were found to be more abundant in productive adult tank water. In addition, nitrate and pH covaried with productive cohorts, explaining 67% of the bacterial populations. The lower abundance of nitrate‐reducing bacteria in unproductive adult tank water could explain detected elevated nitrate levels.

Conclusions

We conclude that microbiome composition and water geochemistry can negatively affect E. scolopes reproductive physiology in closed tank systems, ultimately impacting host‐microbe research using these animals.

Significance and Impact of study

These results identify the tight relationship between the microbiome and geochemistry to E. scolopes. From this study, it may be possible to design probiotic counter‐measures to improve aquaculture conditions for E. scolopes.

Co-culturing Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 allows sustainable denitrifying activities under marine conditions

BACKGROUND

Hyphomicrobium nitrativorans strain NL23 and Methylophaga nitratireducenticrescens strain JAM1 are the principal bacteria involved in the denitrifying activities of a methanol-fed, fluidized-bed marine denitrification system. Strain NL23 possesses the complete denitrification pathway, but cannot grow under marine conditions in pure cultures. Strain JAM1 is a marine bacterium that lacks genes encoding a dissimilatory nitrite (NO2 -) reductase and therefore cannot reduce NO2 -. Here, we report the characterization of some of their physiological traits that could influence their co-habitation. We also perform co-cultures to assess the potential synergy between the two strains under marine and denitrifying conditions.

METHODOLOGY

Anoxic planktonic pure cultures of both strains were grown with different concentrations of nitrate (NO3 -). Anoxic planktonic co-cultures could only be cultured on low NaCl concentrations for strain NL23 to grow. Biofilm co-cultures were achieved in a 500-mL bioreactor, and operated under denitrifying conditions with increasing concentrations of NaCl. NO3 - and NO2 - concentrations and the protein content were measured to derive the denitrification rates. The concentrations of both strains in co-cultures were determined by quantitative PCR (qPCR). Ectoine concentration was measured by mass spectrometry in the biofilm co-culture. The biofilm was visualized by fluorescence in situ hybridization. Reverse-transcription-qPCR and RNA-seq approaches were used to assess changes in the expression profiles of genes involved in the nitrogen pathways in the biofilm cultures.

RESULTS

Planktonic pure cultures of strain JAM1 had a readiness to reduce NO3 - with no lag phase for growth in contrast to pure cultures of strain NL23, which had a 2-3 days lag phase before NO3 - starts to be consumed and growth to occur. Compared to strain NL23, strain JAM1 has a higher µmax for growth and higher specific NO3 - reduction rates. Denitrification rates were twice higher in the planktonic co-cultures than those measured in strain NL23 pure cultures. The biofilm co-cultures showed sustained denitrifying activities and surface colonization by both strains under marine conditions. Increase in ectoine concentrations was observed in the biofilm co-culture with the increase of NaCl concentrations. Changes in the relative transcript levels were observed in the biofilm culture with genes encoding NapA and NapGH in strain NL23. The type of medium had a great impact on the expression of genes involved in the N-assimilation pathways in both strains.

CONCLUSIONS

These results illustrate the capacity of both strains to act together in performing sustainable denitrifying activities under marine conditions. Although strain JAM1 did not contribute in better specific denitrifying activities in the biofilm co-cultures, its presence helped strain NL23 to acclimate to medium with NaCl concentrations >1.0%.

Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls with cpn60-Based Microbiome Profiling

Detection of bacterial DNA within meconium is often cited as evidence supporting in utero colonization. However, many studies fail to adequately control for contamination. We aimed to define the microbial content of meconium under properly controlled conditions. DNA was extracted from 141 meconium samples and subjected to cpn60-based microbiome profiling, with controls to assess contamination throughout. Total bacterial loads of neonatal meconium, infant stool, and controls were compared by 16S rRNA quantitative PCR (qPCR). Viable bacteria within meconium were cultured, and isolate clonality was assessed by pulsed-field gel electrophoresis (PFGE). Meconium samples did not differ significantly from controls with respect to read numbers or taxonomic composition. Twenty (14%) outliers with markedly higher read numbers were collected significantly later after birth and appeared more like transitional stool than meconium. Total bacterial loads were significantly higher in stool than in meconium, which did not differ from that of sequencing controls, and correlated well with read numbers. Cultured isolates were most frequently identified as Staphylococcus epidermidis, Enterococcus faecalis, or Escherichia coli, with PFGE indicating high intraspecies diversity. Our findings highlight the importance of robust controls in studies of low microbial biomass samples and argue against meaningful bacterial colonization in utero. Given that meconium microbiome profiles could not be distinguished from sequencing controls, and that viable bacteria within meconium appeared uncommon and largely consistent with postnatal skin colonization, there does not appear to be a meconium microbiota.

IMPORTANCE Much like the recent placental microbiome controversy, studies of neonatal meconium reporting bacterial communities within the fetal and neonatal gut imply that microbial colonization begins prior to birth. However, recent work has shown that placental microbiomes almost exclusively represent contamination from lab reagents and the environment. Here, we demonstrate that prior studies of neonatal meconium are impacted by the same issue, showing that the microbial content of meconium does not differ from negative controls that have never contained any biological material. Our culture findings similarly supported this notion and largely comprised bacteria normally associated with healthy skin. Overall, our work adds to the growing body of evidence against the in utero colonization hypothesis.

Spatial Variation of Cladophora Epiphytes in the Nan River, Thailand

Cladophora is an algal genus known to be ecologically important. It provides habitats for microorganisms known to provide ecological services such as biosynthesis of cobalamin (vitamin B12) and nutrient cycling. Most knowledge of microbiomes was obtained from studies of lacustrine Cladophora species. However, whether lotic freshwater Cladophora microbiomes are as complex as the lentic ones or provide similar ecological services is not known. To illuminate these issues, we used amplicons of 16S rDNA, 18S rDNA, and ITS to investigate the taxonomy and diversity of the microorganisms associated with replicate Cladophora samples from three sites along the Nan River, Thailand. Results showed that the diversity of prokaryotic and eukaryotic members of Cladophora microbiomes collected from different sampling sites was statistically different. Fifty percent of the identifiable taxa were shared across sampling sites: these included organisms belonging to different trophic levels, decomposers, and heterotrophic bacteria. These heterogeneous assemblages of bacteria, by functional inference, have the potential to perform various ecological functions, i.e., cellulose degradation, cobalamin biosynthesis, fermentative hydrogen production, ammonium oxidation, amino acid fermentation, dissimilatory reduction of nitrate to ammonium, nitrite reduction, nitrate reduction, sulfur reduction, polyphosphate accumulation, denitrifying phosphorus-accumulation, and degradation of aromatic compounds. Results suggested that river populations of Cladophora provide ecologically important habitat for microorganisms that are key to nutrient cycling in lotic ecosystems.

Coupled biodegradation of p-nitrophenol and p-aminophenol in bioelectrochemical system: Mechanism and microbial functional diversity

Biodegradation mechanisms and microbial functional diversity during coupled p-nitrophenol (PNP) and p-aminophenol (PAP) degradation were studied in a bioelectrochemical system. PNP in the biocathode and PAP in the bioanode were almost completely removed within 28hr and 68hr respectively. The degradation followed the steps including hydrating hydroxyalkylation, dehydrogenating carbonylation, and hydrolating ring cleavage, etc. Metagemomic analysis based on the KEGG and eggNOG database annotations revealed the microbial composition and functional genes/enzymes related to phenol degradation in the system. The predominant bacteria genera were Lautropia, Pandoraea, Thiobacillus, Ignavibacterium, Truepera and Hyphomicrobium. The recognized biodegradation genes/enzymes related to pollutant degradation were as follows: pmo, hbd, & ppo for phenol degradation, nzba, amie, & badh for aromatic degradation, and CYP & p450 for xenobiotics degradation, etc. The co-occurrence of ARGs (antibiotic resistant genes), such as adeF, MexJ, ErmF, PDC-93 and Escherichia_coli_mdfA, etc., were annotated in CARD database during the biodegradation process. The Proteobacteria & Actinobacteria phylum was the primary host of both the biodegradation genes & ARGs in this system. The microbial functional diversity ensured the effective biodegradation of the phenol pollutants in the bioelectrochemical system.

Microdiversity characterizes prevalent phylogenetic clades in the glacier-fed stream microbiome

Glacier-fed streams (GFSs) are extreme and rapidly vanishing ecosystems, and yet they harbor diverse microbial communities. Although our understanding of the GFS microbiome has recently increased, we do not know which microbial clades are ecologically successful in these ecosystems, nor do we understand potentially underlying mechanisms. Ecologically successful clades should be more prevalent across GFSs compared to other clades, which should be reflected as clade-wise distinctly low phylogenetic turnover. However, methods to assess such patterns are currently missing. Here we developed and applied a novel analytical framework, “phyloscore analysis”, to identify clades with lower spatial phylogenetic turnover than other clades in the sediment microbiome across twenty GFSs in New Zealand. These clades constituted up to 44% and 64% of community α-diversity and abundance, respectively. Furthermore, both their α-diversity and abundance increased as sediment chlorophyll a decreased, corroborating their ecological success in GFS habitats largely devoid of primary production. These clades also contained elevated levels of putative microdiversity than others, which could potentially explain their high prevalence in GFSs. This hitherto unknown microdiversity may be threatened as glaciers shrink, urging towards further genomic and functional exploration of the GFS microbiome.

Internal microbial zonation during the massive growth of marimo, a lake ball of Aegagropila linnaei in Lake Akan

Marimo (lake ball) is an uncommon ball-like aggregation of the green alga, Aegagropila linnaei. Although A. linnaei is distributed in fresh and brackish waters in the northern hemisphere, marimo colonies are found only in particular habitats. Here, we report the bacterial communities inside various sizes and aggregating structures of natural marimo collected from Lake Akan, Japan. We observed multi-layers composed of sediment particles only in the sizable radial-type marimo with >20 cm diameter and not in the tangled-type marimo. The deeper layers were enriched by Nitrospira, potential sulfur-oxidizing bacteria, and sulfate-reducing bacteria. Microorganisms of the multi-layers would form biofilms incorporating nearby sediment, which would function as microbial “seals” within large radial-type marimo. These findings provide clues to deciphering the growth of endangered marimo.

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The radial type of marimo (lake ball) can grow to over 20 cm in diameter

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The sizable radial-type marimo develops the internal multi-layers and hollow structure

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The layers provide different diverse microbiomes and structural strength

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The internal multi-layers support the massive growth of the radial-type marimo

Total and Metabolically Active Microbial Community of Aerobic Granular Sludge Systems Operated in Sequential Batch Reactors: Effect of Pharmaceutical Compounds

Two aerobic granular sludge (AGS) sequential batch reactors were operated at a mild (15 °C) temperature for 180 days. One of those bioreactors was exposed to a mixture of diclofenac, naproxen, trimethoprim, and carbamazepine. The AGS system, operating under pressure from emerging contaminants, showed a decrease in COD, BOD5, and TN removal capacity, mainly observed during the first 100 days, in comparison with the removal ratios detected in the control bioreactor. After an acclimatisation period, the removal reached high-quality effluent for COD and TN, close to 95% and 90%, respectively. In the steady-state period, trimethoprim and diclofenac were successfully removed with values around 50%, while carbamazepine and naproxen were more recalcitrant. The dominant bacterial OTUs were affected by the presence of a mixture of pharmaceutical compounds, under which the dominant phylotypes changed to OTUs classified among the Pseudomonas, Gemmobacter, and Comamonadaceae. The RT-qPCR and qPCR results showed the deep effects of pharmaceutical compounds on the number of copies of target genes. Statistical analyses allowed for linking the total and active microbial communities with the physico-chemical performance, describing the effects of pharmaceutical compounds in pollution degradation, as well as the successful adaptation of the system to treat wastewater in the presence of toxic compounds.

Bacterial community in saline farmland soil on the Tibetan plateau: responding to salinization while resisting extreme environments

Background

Salinization damages the health of soil systems and reduces crop yields. Responses of microbial communities to salinized soils and their functional maintenance under high salt stress are valuable scientific problems. Meanwhile, the microbial community of the salinized soil in the plateau environment is less understood. Here, we applied metagenomics technology to reveal the structure and function of microorganisms in salinized soil of the Tibetan Plateau.

Results

The diversity of composition and function of microbial community in saline soil have changed significantly. The abundances of chemoautotrophic and acidophilic bacteria comprising Rhodanobacter, Acidobacterium, Candidatus Nitrosotalea, and Candidatus Koribacter were significantly higher in saline soil. The potential degradation of organic carbon in the saline soil, as well as the production of NO and N₂O via denitrification, and the production of sulfate by sulfur oxidation were significantly higher than the non-saline soil. Both types of soils were rich in genes encoding resistance to environmental stresses (i.e., cold, ultraviolet light, and hypoxia in Tibetan Plateau). The resistance of the soil microbial communities to the saline environment is based on the absorption of K⁺ as the main mechanism, with cross-protection proteins and absorption buffer molecules as auxiliary mechanisms in our study area. Network analysis showed that functional group comprising chemoautotrophic and acidophilic bacteria had significant positive correlations with electrical conductivity and total sulfur, and significant negative correlations with the total organic carbon, pH, and available nitrogen. The soil moisture, pH, and electrical conductivity are likely to affect the bacterial carbon, nitrogen, and sulfur cycles.

Conclusions

These results indicate that the specific environment of the Tibetan Plateau and salinization jointly shape the structure and function of the soil bacterial community, and that the bacterial communities respond to complex and harsh living conditions. In addition, environmental feedback probably exacerbates greenhouse gas emissions and accelerates the reduction in the soil pH. This study will provide insights into the microbial responses to soil salinization and the potential ecological risks in the special plateau environment.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02190-6.

Intracellular bacteria are common and taxonomically diverse in cultured and in hospite algal endosymbionts of coral reefs

Corals house a variety of microorganisms which they depend on for their survival, including endosymbiotic dinoflagellates (Symbiodiniaceae) and bacteria. While cnidarian–microorganism interactions are widely studied, Symbiodiniaceae–bacteria interactions are only just beginning to receive attention. Here, we describe the localization and composition of the bacterial communities associated with cultures of 11 Symbiodiniaceae strains from nine species and six genera. Three-dimensional confocal laser scanning and electron microscopy revealed bacteria are present inside the Symbiodiniaceae cells as well as closely associated with their external cell surface. Bacterial pure cultures and 16S rRNA gene metabarcoding from Symbiodiniaceae cultures highlighted distinct and highly diverse bacterial communities occur intracellularly, closely associated with the Symbiodiniaceae outer cell surface and loosely associated (i.e., in the surrounding culture media). The intracellular bacteria are highly conserved across Symbiodiniaceae species, suggesting they may be involved in Symbiodiniaceae physiology. Our findings provide unique new insights into the biology of Symbiodiniaceae.

Biological Reduction of Nitric Oxide for Efficient Recovery of Nitrous Oxide as an Energy Source

Chemical absorption-biological reduction based on Fe(II)EDTA is a promising technology to remove nitric oxide (NO) from flue gases. However, limited effort has been made to enable direct energy recovery from NO through production of nitrous oxide (N₂O) as a potential renewable energy rather than greenhouse gas. In this work, the enhanced energy recovery in the form of N₂O via biological NO reduction was investigated by conducting short-term and long-term experiments at different Fe(II)EDTA-NO and organic carbon levels. The results showed both NO reductase and N₂O reductase were inhibited at Fe(II)EDTA-NO concentration up to 20 mM, with the latter being inhibited more significantly, thus facilitating N₂O accumulation. Furthermore, N₂O accumulation was enhanced under carbon-limiting conditions because of electron competition during short-term experiments. Up to 47.5% of NO-N could be converted to gaseous N₂O-N, representing efficient N₂O recovery. Fe(II)EDTA-NO reduced microbial diversity and altered the community structure toward Fe(II)EDTA-NO-reducing bacteria-dominated culture during long-term experiments. The most abundant bacterial genus Pseudomonas, which was able to resist the toxicity of Fe(II)EDTA-NO, was significantly enriched, with its relative abundance increased from 1.0 to 70.3%, suggesting Pseudomonas could be the typical microbe for the energy recovery technology in NO-based denitrification.