Seven novel species of Acinetobacter isolated from activated sludge

Genome sequences of Acinetobacter phage At2 and its host Acinetobacter tandoii W4-4-4

We present the genome sequences of Acinetobacter phage At2 and its host Acinetobacter tandoii strain W4-4-4, both isolated from a tropical mangrove swamp in Singapore. This report highlights the genetic features of both organisms, including antimicrobial resistance genes.

Stable partial nitrification was achieved for nitrogen removal from municipal wastewater by gel immobilization: A pilot-scale study

As an energy and carbon saving process for nitrogen removal from wastewater, the partial nitrification and denitrification process (PN/D) has been extensively researched. However, achieving stable PN in municipal wastewater has always been challenging. In this study, a gel immobilized PN/D nitrogen removal process (GI-PN/D) was established. A 94 days pilot-scale experiment was conducted using real municipal wastewater with an ammonia concentration of 43.5 ± 5.3 mg N/L at a temperature range of 11.3-28.7℃. The nitrogen removal performance and associated pathways, shifts in the microbial community as well as sludge yield were investigated. The results were as follows: the effluent TN and COD were 0.6 ± 0.4 mg/L and 31.1 ± 3.8 mg/L respectively, and the NAR exceeding 95%. GI-PN/D achieved deep nitrogen removal of municipal wastewater through stable PN without taking any other measures. The primary pathways for nitrogen removal were identified as denitrification, simultaneous nitrification-denitrification, and aerobic denitrification. High-throughput sequencing analysis revealed that the immobilized fillers facilitated the autonomous enrichment of functional bacteria in each reactor, effectively promoting the dominance and stability of the microbial communities. In addition, GI-PN/D had the characteristic of low sludge yield, with an average sludge yield of 0.029 kg SS/kg COD. This study provides an effective technical for nitrogen removal from municipal wastewater through PN.

Genome analysis of manure and soil-dwelling Acinetobacter strains indicates potential health risks associated with antibiotic resistance and virulence factors

The genus Acinetobacter includes opportunistic pathogenic species of increasing clinical importance due to their ability to resist multiple antibiotics and to face multiple environmental stresses. Here, comprehensive whole-genome analysis was used to reveal the presence of genes potentially related to pathogenicity in 11 tetracycline-resistant Acinetobacter isolates from manure of dairy cows under tetracycline and amoxicillin prophylaxis and from soils affected by this manure. The isolates were identified as Acinetobacter pseudolwoffii, A. gerneri, A. gandensis, and A. amyesii and screened their genomes for the presence of genes related to host colonization, infection, or environmental persistence. We detected 164 genes of antimicrobial resistance, virulence factors, mobile genetic elements, or biofilm formation. All isolates were predicted to be human pathogens with high probability (0.7-0.8) and the manure isolates identified as A. pseudolwoffii carried a top-risk human-associated aminoglycoside resistance gene. The phenotypic characterization of the isolates showed that they could all grow at 37 °C, some up to 41 °C, and that they showed differential susceptibility to several antibiotics, with one isolate identified as A. gandensis being multi-resistant. Our analyses suggest that environmental Acinetobacter strains from fresh manure and manured soils possess risky antibiotic-resistance genes and phenotypic traits of clinical relevance indicating potential pathogenicity.

Postmortem Findings in Free-Ranging North American Beavers (Castor canadensis) Reveal Potential Threats to California's Freshwater Ecosystems

North American beavers (Castor canadensis) are semi-aquatic rodents recognized as keystone species because they increase the diversity of freshwater ecosystems. This study aimed to characterize the mortality and pathological findings in free-ranging beavers in California and, based on these results, identify potential threats to freshwater ecosystems. This study included 18 beavers submitted for postmortem examination at the California Animal Health and Food Safety Laboratory, UC Davis, between 2008 and 2024. Gross and microscopic examinations, and bacteriological, parasitological, immunohistochemical, and molecular techniques, were used as tools to diagnose the cause of death/reason for euthanasia and comorbidities in the beavers. Baylisascaris spp.-associated or -suspected encephalitis was the most prevalent (9/18, 50%) cause of mortality/reason for euthanasia, followed by bacterial infections in six individuals. In these six animals, bacterial bronchopneumonia was diagnosed in two (Staphylococcus aureus and a mix of Gram-negative and -positive bacterial infection) and Listeria monocytogenes encephalitis, bacterial myofascitis (Aeromonas bestiarum and Pasteurella multocida), bacterial encephalitis (Acinetobacter towneri), and tularemia (Francisella tularensis) were diagnosed in one beaver each. Three animals died or were euthanized due to non-infectious causes, including motor vehicle trauma, squamous cell carcinoma, and capture cardiomyopathy. Endoparasitism was the main comorbidity, including granulomatous hepatitis caused by a suspected capillarid species, cerebral toxoplasmosis, Giardia infection, gastric nematodiasis, and cecal trematodiasis. In California, beavers are exposed to various pathogens that represent threats to humans, domestic animals, and wildlife. Since the interspecies transmission of these pathogens occurs in rivers, streams, lakes, and ponds, we suggest that studying beaver health can reflect freshwater ecosystem health. This study also indicates that the translocation of beavers to new areas without consideration and/or mitigation represents a potential risk of pathogen introduction.

In silico characterization of defense system hotspots in Acinetobacter spp

The bacteria-phage arm race drives the evolution of diverse bacterial defenses. This study identifies and characterizes the defense hotspots in Acinetobacter baumannii using a reference-free approach. Among 4383 high-quality genomes, we found a total of 17,430 phage defense systems and with 54.54% concentrated in 21 hotspots. These hotspots exhibit distinct preferences for different defense systems, and co-occurrence patterns suggest synergistic interactions. Additionally, the mobile genetic elements are abundant around these hotspots, likely facilitating horizontal transfer and evolution of defense systems. The number of hotspots increases in species phylogenetically closer to Acinetobacter baumannii, but the number of defense systems per hotspot varies due to particular selective pressures. These findings provide critical insights into the genetic organization of phage defense systems, contributing to a broader understanding of bacterial immunity and the evolutionary dynamics that shape Acinetobacter genomes. This knowledge lays the foundation for developing targeted interventions  to combat antibiotic resistance Acinetobacter baumannii.

Spatio-temporal plasticity of gill microbiota in estuarine fish

Coastal marine and estuarine systems are subject to enormous endogenous and exogenous pressures, particularly climate change, while at the same time being highly productive sources and nurseries for fish populations. Interactions between host and microbiome are increasingly recognized for their importance for fish health, with growing evidence indicating that increasing environmental pressures impact host resilience and favor the raise of opportunistic bacterial taxa. The microbial composition of the gill mucus reflects environmental conditions and represents an entry route for pathogens into the fish body. High-throughput sequencing of prokaryotic populations from 250 samples of two fish species with highly different habitat preferences, as well as seasonal and spatial distributions in the Elbe estuary system, allowed us to describe the variation of the microbiota along a salinity gradient and under fluctuating environmental conditions. The analysis of estuarine fish core microbiota in relation to variable bacterial components indicated dysbiotic states under sustained hypoxia and high nutrient loads largely driven by increased prevalence of facultatively aerobic (Acinetobacter) and anaerobic heterotrophs (Shewanella, Aeromonas). By correlating bacterial abundances with environmental and physiological parameters in a co-occurrence network approach, we describe plasticity in microbiota composition, identify potential biomarkers for fish health monitoring and reconstruct movement patterns of the fish. Our results can help to shape future minimal-invasive and cost-effective monitoring programs, and identify factors that need to be controlled in the estuary to promote fish and stock health.

Analytical methods for quantifying PS and PVC Nanoplastic attachment to activated sludge Bacteria and their impact on community structure

Nanoplastics are anticipated to be ubiquitous in various environmental compartments. However, challenges in analytical methods hinder our understanding of risks related to specific nanplastics characteristics such as size and chemical compositions, and interactions between nanoplastics and microorganisms. In this study, we applied fit-for-purpose analytical methods and techniques to understand how nanoplastic chemical composition influences their interaction with bacteria collected from activated sludge. When exposed to polystyrene (PS) and polyvinyl chloride (PVC) nanoplastics for 5 days, the nanoplastics attached to the bacteria. Specifically, on day 1, there was a significant predominance of PS nanoplastics over PVC ones of similar size and shape, possibly due to differences in their chemical composition. After 5 days, there is a substantial decrease in nanoplastics attached to bacteria, suggesting bacterial defence mechanisms may reduce particles attachment over time. The overall bacterial community structure demonstrated a high degree of resilience. This resilience highlights the ability of microbial communities to maintain their structure despite nanoplastic stressors, as evidenced by consistent alpha diversity, PCoA, and PERMANOVA results. Understanding these mechanisms is crucial for assessing nanoplastic fate and thus environmental impacts.

Monitoring Ammonium Polyphosphate (APP) Biodegradation by Acinetobacter nosocomialis D-3 Using DAPI

Ammonium polyphosphate (APP), a pivotal constituent within environmentally friendly flame retardants, exhibits notable decomposition susceptibility and potentially engenders ecological peril. Consequently, monitoring the APP concentration to ensure product integrity and facilitate the efficacious management of wastewater from production processes is of great significance. A fluorescent assay was devised to swiftly discern APP utilizing 4',6'-diamino-2-phenylindole (DAPI). With increasing APP concentrations, DAPI undergoes intercalation within its structure, emitting pronounced fluorescence. Notably, the flame retardant JLS-PNA220-A, predominantly comprising APP, was employed as the test substrate. Establishing a linear relationship between fluorescence intensity (F-F0) and JLS-PNA220-A concentration yielded the equation y = 76.08x + 463.2 (R2 = 0.9992), with a LOD determined to be 0.853 mg/L. The method was used to assess the degradation capacity of APP-degrading bacteria. Strain D-3 was isolated, and subsequent analysis of its 16S DNA sequence classified it as belonging to the Acinetobacter genus. Acinetobacter nosocomialis D-3 demonstrated superior APP degradation capabilities under pH 7 at 37 °C, with degradation rates exceeding 85% over a four-day cultivation period. It underscores the sensitivity and efficacy of the proposed method for APP detection. Furthermore, Acinetobacter nosocomialis D-3 exhibits promising potential for remediation of residual APP through environmental biodegradation processes.

A new and promiscuous α/β hydrolase from Acinetobacter tandoii DSM 14970 T inactivates the mycotoxin ochratoxin A

The presence of ochratoxin A (OTA) in food and feed represents a serious concern since it raises severe health implications. Bacterial strains of the Acinetobacter genus hydrolyse the amide bond of OTA yielding non-toxic OTα and L-β-phenylalanine; in particular, the carboxypeptidase PJ15_1540 from Acinetobacter sp. neg1 has been identified as an OTA-degrading enzyme. Here, we describe the ability to transform OTA of cell-free protein extracts from Acinetobacter tandoii DSM 14970 T, a strain isolated from sludge plants, and also report on the finding of a new and promiscuous α/β hydrolase (ABH), with close homologs highly distributed within the Acinetobacter genus. ABH from A. tandoii (AtABH) exhibited amidase activity against OTA and OTB mycotoxins, as well as against several carboxypeptidase substrates. The predicted structure of AtABH reveals an α/β hydrolase core composed of a parallel, six-stranded β-sheet, with a large cap domain similar to the marine esterase EprEst. Further biochemical analyses of AtABH reveal that it is an efficient esterase with a similar specificity profile as EprEst. Molecular docking studies rendered a consistent OTA-binding mode. We proposed a potential procedure for preparing new OTA-degrading enzymes starting from promiscuous α/β hydrolases based on our results. KEY POINTS: • AtABH is a promiscuous αβ hydrolase with both esterase and amidohydrolase activities • AtABH hydrolyses the amide bond of ochratoxin A rendering nontoxic OTα • Promiscuous αβ hydrolases are a possible source of new OTA-degrading enzymes.

Acinetobacter entericus sp. nov., isolated from the gut of plastic-eating insect larvae Zophobas atratus

A Gram-negative, non-motile and rod-shaped strain, BIT-DXN8T, was isolated from the gut of plastic-eating insect larvae Zophobas atratus. The taxonomic position of this new isolate was examined by using a polyphasic approach. A preliminary analysis based on the 16S rRNA gene sequence (1411 bp) indicated that the most similar strain to BIT-DXN8T was Acinetobacter bouvetii DSM 14964T (98.5%), followed by Acinetobacter haemolyticus CIP 64.3T (98.2%) and Acinetobacter pullicarnis S23T (98.2%). The results of phylogenetic analyses, based on the 16S rRNA gene, concatenated sequences of five housekeeping genes (fusA, gyrB, recA, rplB and rpoB) and genome sequences, placed strain BIT-DXN8T in a separate lineage among the genus Acinetobacter of the family Moraxellaceae. The average nucleotide identity and digital DNA-DNA hybridization values of the strain when compared to all other species within the genus Acinetobacter were below 96 and 70 %, respectively. The physiological and biochemical tests confirm the affiliation of strain BIT-DXN8T to the present species within the genus Acinetobacter, but with some specific phenotypic differences. Therefore, strain BIT-DXN8T is considered to represent a novel species, for which the name Acinetobacter entericus sp. nov. is proposed. The type strain is BIT-DXN8T (=CCTCC AB 2022117T=KCTC 92696T).

Method of selective isolation of <i>Acinetobacter baylyi</i> from river water

The aim of the study is to increase the selectivity of isolating Acinetobacter baylyi from river water. For developing a selective culture medium, we used 5 strains of A. baylyi, 4 of which were isolated from the water of the river Neva, 1 from clinical material. A. baylyi strains were identified by a combination of phenotypic features and/or using the mass spectrometric method (MALDI-ToF MS). In preliminary studies we found that the bacteria A. baylyi utilizes no L-phenylalanine as a single source of carbon and nitrogen, as well as the only source of carbon in a medium with mineral nitrogen sources, but utilizes L-phenylalanine as the only source of nitrogen only if it is supplemented with ethanol as the only source of carbon. Based on this A. baylyi property, a selective medium was developed for the isolation of these bacteria from river water. Composition and preparation of liquid selective medium were as follows: 1 liter of distilled water added with L-phenylalanine (CAS 63-91-2) 2.0 (g/l); NaCI 5.0; Na2SO4 2.0; KH2PO4 1.0; K2HPO4 2.5; MgSO4 0.1; dissolved while heating, boiled for 5 minutes, 4 ml of 96-degree ethanol was added to a warm medium, pH 7.20.2 assessed; 40 ml were poured into sterile vials. Dense selective medium: the same ingredients and extra 15.0 g of agar are added to 1 liter of distilled water; with similar preparation technique, the medium is poured into sterile Petri dishes. Method of application of selective nutrient medium for isolation of A. baylyi from river water: water from the river Neva is seeded in a volume of 10 ml into a vial with 40 ml of liquid selective medium, incubated in aerobic conditions at 28С for 48 h, then the enriched material from the flask is placed with a bacteriological loop onto the surface of same dense selective medium in two flasks; incubated in aerobic conditions at 28С for 48 h. 10 isolated colonies are selected for subsequent identification, they are transplanted into sectors of nutrient agar, incubated at 28С 24 h and isolates are identified by a complex of phenotypic characteristic of A. baylyi, and/or by the MALDI-ToF MS method. In this case, 19 isolates from 20 were identified as A. baylyi (95% of isolates). A study using this technique of three more water samples from the river Neva showed the results of the same narrowly selective orientation 9095% of the isolates were bacteria A. baylyi.

Impact of petroleum refinery on aquatic ecosystem of Skikda Bay (Algeria): Diversity and abundance of viable bacterial strains

This paper reports a study on the impact of petroleum refinery effluents on the bacterial load and diversity of the aquatic ecosystem in Skikda Bay (Algeria). The results showed a large spatiotemporal variation in the isolated bacterial species. This difference between stations and seasons could be attributed to environmental factors and to the pollution rate at the different sampling sites. Statistical analysis results showed that physicochemical parameters such as pH, electrical conductivity and salinity have a very significant effect on the microbial load (p < 0.001), while hydrocarbon pollution has a significant effect on the diversity of bacterial species (p < 0.05). In total 75 bacteria were isolated from six sampling sites during the four seasons. A significant spatiotemporal richness and diversity was observed in water samples. A total of 42 strains belonging to 18 bacterial genera were identified. Most of these genera belong to the class of Proteobacteria.

A comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains

Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species. In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.

Kinetic characterization of a new phenol degrading Acinetobacter towneri strain isolated from landfill leachate treating bioreactor

The objective of this study was to establish and to mathematically describe the phenol degrading properties of a new Acinetobacter towneri CFII-87 strain, isolated from a bioreactor treating landfill leachate. For this purpose, the biokinetic parameters of phenol biodegradation at various initial phenol concentrations of the A. towneri CFII-87 strain have been experimentally measured, and four different mathematical inhibition models (Haldane, Yano, Aiba and Edwards models) have been used to simulate the substrate-inhibited phenol degradation process. The results of the batch biodegradation experiments show that the new A. towneri CFII-87 strain grows on and metabolizes phenol up to 1000 mg/L concentration, manifests significant substrate inhibition and lag time only at concentrations above 800 mg/L phenol, and has a maximum growth rate at 300 mg/L initial phenol concentration. The comparison of the model predictions with the experimental phenol and biomass data revealed that the Haldane, Aiba and Edwards models can be used with success to describe the phenol biodegradation process by A. towneri CFII-87, while the Yano model, especially at higher initial phenol concentrations, fails to describe the process. The best performing inhibition model was the Edwards model, presenting correlation coefficients of R² > 0.98 and modelling efficiency of ME > 0.94 for the prediction of biomass and phenol concentrations on the validation datasets. The calculated biokinetic model parameters place this new strain among the bacteria with the highest tolerance towards phenol. The results suggest that the A. towneri CFII-87 strain can potentially be used in the treatment of phenolic wastewaters.

Acinetobacter tibetensis sp. nov., Isolated from a Soil Under a Greenhouse in Tibet

A Gram-stain-negative, light yellow, aerobic, non-motile, short rod-shaped bacterium named strain Y-23^T with iprodione-degrading capability was isolated from a soil under a greenhouse in Tibet, PR China. Strain Y-23^T grew at 4-37 ℃ and pH 5.0-9.0 (optimum, 25 ℃ and pH 7.0) with 0-3% (w/v) NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene and chromosome genome indicated that strain Y-23^T formed a stable evolutionary branch with Acinetobacter tandoii DSM 14970^T. The 16S rRNA gene similarity, digital DNA-DNA hybridization and average nucleotide identity values between strain Y-23^T and Acinetobacter tandoii DSM 14970^T were 98.31%, 43.2% and 91.2%, respectively. The genome size was 3.39 Mbp with a genomic DNA G+C content of 40.59 mol%. The predominant fatty acids were C_18:1 ω9c, Summed feature 3 (C_16:1 ω7c/C_16:1 ω6c), C_12:0, C_12:0 3-OH and C_16:0. The polar lipids were diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl choline, unidentified phospholipid, four unidentified aminophospholipids and two unidentified lipids. The isoprenoid quinone was Q-8 (19.43%) and Q-9 (80.57%). Based on phenotypic, phylogenetic, and genotypic data, strain Y-23^T is considered to represent a novel species of the genus Acinetobacter, for which the name Acinetobacter tibetensis sp. nov. is proposed. The type strain is Y-23^T (= CICC 25150^T = JCM 35630^T).

Antibiotic concentrations in raw hospital wastewater surpass minimal selective and minimum inhibitory concentrations of resistant Acinetobacter baylyi strains

Antibiotics are essential for modern medicine, they are employed frequently in hospitals and, therefore, present in hospital wastewater. Even in concentrations, that are lower than the minimum inhibitory concentrations (MICs) of susceptible bacteria, antibiotics may exert an influence and select resistant bacteria, if they exceed the MSCs (minimal selective concentrations) of resistant strains. Here, we compare the MSCs of fluorescently labelled Acinetobacter baylyi strains harboring spontaneous resistance mutations or a resistance plasmid with antibiotic concentrations determined in hospital wastewater. Low MSCs in the μg/L range were measured for the quinolone ciprofloxacin (17 μg/L) and for the carbapenem meropenem (30 μg/L). A 24 h continuous analysis of hospital wastewater showed daily fluctuations of the concentrations of these antibiotics with distinctive peaks at 7-8 p.m. and 5-6 a.m. The meropenem concentrations were always above the MSC and MIC values of A. baylyi. In addition, the ciprofloxacin concentrations were in the range of the lowest MSC for about half the time. These results explain the abundance of strains with meropenem and ciprofloxacin resistance in hospital wastewater and drains.

Biocides used as material preservatives modify rates of de novo mutation and horizontal gene transfer in bacteria

Antimicrobial resistance (AMR) is a global health problem with the environment being an important compartment for the evolution and transmission of AMR. Previous studies showed that de-novo mutagenesis and horizontal gene transfer (HGT) by conjugation or transformation - important processes underlying resistance evolution and spread - are affected by antibiotics, metals and pesticides. However, natural microbial communities are also frequently exposed to biocides used as material preservatives, but it is unknown if these substances induce mutagenesis and HGT. Here, we show that active substances used in material preservatives can increase rates of mutation and conjugation in a species- and substance-dependent manner, while rates of transformation are not increased. The bisbiguanide chlorhexidine digluconate, the quaternary ammonium compound didecyldimethylammonium chloride, the metal copper, the pyrethroid-insecticide permethrin, and the azole-fungicide propiconazole increase mutation rates in Escherichia coli, whereas no increases were identified for Bacillus subtilis and Acinetobacter baylyi. Benzalkonium chloride, chlorhexidine and permethrin increased conjugation in E. coli. Moreover, our results show a connection between the RpoS-mediated general stress and the RecA-linked SOS response with increased rates of mutation and conjugation, but not for all biocides. Taken together, our data show the importance of assessing the contribution of material preservatives on AMR evolution and spread.

The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany

Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.

Imported Pet Reptiles and Their “Blind Passengers”—In-Depth Characterization of 80 Acinetobacter Species Isolates

Reptiles are popular pet animals and important food sources, but the trade of this vertebrate class is—besides welfare and conservation—under debate due to zoonotic microbiota. Ninety-two shipments of live reptiles were sampled during border inspections at Europe’s most relevant transshipment point for the live animal trade. Acinetobacter spp. represented one significant fraction of potentially MDR bacteria that were further analyzed following non-selective isolation or selective enrichment from feces, urinate, or skin samples. Taxonomic positions of respective isolates were confirmed by MALDI-TOF MS and whole-genome sequencing analysis (GBDP, dDDH, ANIb, and rMLST). The majority of the 80 isolates represented established species; however, a proportion of potentially novel taxa was found. Antimicrobial properties and genome-resistance gene screening revealed novel and existing resistance mechanisms. Acinetobacter spp. strains were most often resistant to 6–10 substance groups (n = 63) in vitro. Resistance to fluorchinolones (n = 4) and colistin (n = 7), but not to carbapenems, was noted, and novel oxacillinase variants (n = 39) were detected among other genes. Phylogenetic analysis (MLST) assigned few isolates to the known STs (25, 46, 49, 220, and 249) and to a number of novel STs. No correlation was found to indicate that MDR Acinetobacter spp. in reptiles were associated with harvesting mode, e.g., captive-bred, wild-caught, or farmed in natural ecosystems. The community of Acinetobacter spp. in healthy reptiles turned out to be highly variable, with many isolates displaying a MDR phenotype or genotype.

Biological recovery of phosphorus from waste activated sludge via alkaline fermentation and struvite biomineralization by Brevibacterium antiquum

Struvite biomineralization is a promising method for phosphorus recovery from wastewater treatment plant streams, and the growth of responsible microorganisms in mixed cultures is one of the most critical points for applying this process in pilot and full-scale. This study aimed to investigate the growth and bio-struvite production of Brevibacterium antiquum in mixed sludge culture. Alkaline fermentation was applied at different pH conditions to enhance the phosphorus content of sludge for an efficient recovery, and pH 8 was determined as the most feasible considering the phosphorus release and sludge characteristics. Growth optimization studies showed that NaCl's presence decreases the growth rate of Brevibacterium antiquum and bio-struvite production. At the same time, pH in the range of 6.8-8.2 did not alter the growth significantly. In addition, studies showed the ability of Brevibacterium antiquum in unsterilized fermented sludge centrate to grow and recover the phosphorus as struvite. Thus, our results indicated the potential of struvite biomineralization in full-scale wastewater treatment plants.

Isolation and characterization of bacteria from activated sludge capable of degrading 17α-ethinylestradiol, a contaminant of high environmental concern

The compound 17α-ethinylestradiol (EE2) is a synthetic oestrogen which is classified as a group 1 carcinogen by the World Health Organization. Together with other endocrine disruptor compounds, EE2 has been included in the surface water Watch List by the European Commission, since it causes severe adverse effects in ecosystems. Thus, it became a high priority to find or improve processes such as biodegradation of EE2 to completely remove this drug from the wastewater treatment plants (WWTPs). The present study aimed at the isolation of bacteria capable of degrading EE2 using environmental samples, namely a sludge from the Faro Northwest WWTP. Four isolates with ability to grow in the presence of 50 mg l^-1 EE2 were obtained. The analysis of 16SrRNA gene sequences identified the isolated bacteria as Acinetobacter bouvetii, Acinetobacter kookii, Pantoea agglomerans and Shinella zoogloeoides. The results of biodegradation assays showed that Acinetobacter bouvetii, Acinetobacter kookii, Pantoea agglomerans and Shinella zoogloeoides were able to degrade 47±4 %, 55±3 %, 64±4% and 35±4 %, respectively of 13 mg l^-1 EE2 after 168 h at 28 °C. To the best of our knowledge, these bacterial isolates were identified as EE2 degraders for the first time. In a preliminary experiment on the identification of metabolic products resulting from EE2 degradation products such as estrone (E1), γ-lactone compounds, 2-pentanedioic acid and 2-butenedioic acid an intermediate metabolite of the TCA cycle, were detected.

Genome Sequence of Acinetobacter towneri Strain DSM 16313, Previously Known as the Proposed Type Strain of Acinetobacter seohaensis

Acinetobacter species are widely distributed in the environment and clinical settings worldwide. We report the 2.99-Mbp draft genome sequence of Acinetobacter towneri strain DSM 16313, which was isolated from seawater in South Korea and proposed as a type strain of Acinetobacter seohaensis. Genome comparisons demonstrated that A. seohaensis should be reclassified as A. towneri.

Identification of Microorganisms from Several Surfaces by MALDI-TOF MS: P. aeruginosa Is Leading in Biofilm Formation

New ecological trends and changes in consumer behavior are known to favor biofilm formation in household appliances, increasing the need for new antimicrobial materials and surfaces. Their development requires laboratory-cultivated biofilms, or biofilm model systems (BMS), which allow for accelerated growth and offer better understanding of the underlying formation mechanisms. Here, we identified bacterial strains in wildtype biofilms from a variety of materials from domestic appliances using matrix-assisted laser desorption/ionization-time of flight mass spectroscopy (MALDI-TOF-MS). Staphylococci and pseudomonads were identified by MALDI-TOF-MS as the main genera in the habitats and were analyzed for biofilm formation using various in vitro methods. Standard quantitative biofilm assays were combined with scanning electron microscopy (SEM) to characterize biofilm formation. While Pseudomonas putida, a published lead germ, was not identified in any of the collected samples, Pseudomonas aeruginosa was found to be the most dominant biofilm producer. Water-born Pseudomonads were dominantly found in compartments with water contact only, such as in detergent compartment and detergent enemata. Furthermore, materials in contact with the washing load are predominantly colonized with bacteria from the human.

Acinetobacter baylyi ADP1-naturally competent for synthetic biology

Acinetobacter baylyi ADP1 is a non-pathogenic soil bacterium known for its metabolic diversity and high natural transformation and recombination efficiency. For these features, A. baylyi ADP1 has been long exploited in studying bacterial genetics and metabolism. The large pool of information generated in the fundamental studies has facilitated the development of a broad range of sophisticated and robust tools for the genome and metabolic engineering of ADP1. This mini-review outlines and describes the recent advances in ADP1 engineering and tool development, exploited in, for example, pathway and enzyme evolution, genome reduction and stabilization, and for the production of native and non-native products in both pure and rationally designed multispecies cultures. The rapidly expanding toolbox together with the unique features of A. baylyi ADP1 provide a strong base for a microbial cell factory excelling in synthetic biology applications where evolution meets rational engineering.

An Update on Wastewater Multi-Resistant Bacteria: Identification of Clinical Pathogens Such as Escherichia coli O25b:H4-B2-ST131-Producing CTX-M-15 ESBL and KPC-3 Carbapenemase-Producing Klebsiella oxytoca

Wastewater treatment plants (WWTPs) are significant reservoirs of bacterial resistance. This work aims to identify the determinants of resistance produced by Gram-negative bacteria in the influent and effluent of two WWTPs in Portugal. A total of 96 wastewater samples were obtained between 2016 and 2019. The numbers of total aerobic and fecal contamination bacteria were evaluated, and genomic features were searched by polymerase chain reaction (PCR) and Next-Generation Sequencing (NGS). Enterobacteriaceae corresponded to 78.6% (n = 161) of the 205 isolates identified by 16sRNA. The most frequent isolates were Escherichia spp. (57.1%, n = 117), followed by Aeromonas spp. (16.1%, n = 33) and Klebsiella spp. (12.7%, n = 26). The remaining 29 isolates (14.1%) were distributed across 10 different genera. Among the 183 resistant genes detected, 54 isolates produced extended spectrum β-lactamases (ESBL), of which bla_CTX-M-15 was predominant (37 isolates; 68.5%). A KPC-3 carbapenemase-producing K. oxytoca was identified (n = 1), with bla_KPC-3 included in a transposon Tn4401 isoform b. A higher number of virulence genes (VG) (19 genes) was found in the E. coli 5301 (O25b-ST131-B2) isolate compared with a commensal E. coli 5281 (O25b-ST410-A) (six genes). Both shared five VG [Enterobactin; Aerobactin, CFA/1 (clade α); Type1 (clade γ1); Type IV]. In conclusion, this work highlights the role of relevant clinical bacteria in WWTPs, such as KPC-3-producing K. oxytoca, and, for the first time, a CTX-M-15-producing Ochromobactrum intermedium, a human opportunistic pathogen, and a SED-1-producing Citrobacter farmeri, an uncommon CTX-M-type extended-spectrum beta-lactamase.

Acinetobacter stercoris sp. nov. isolated from output source of a mesophilic german biogas plant with anaerobic operating conditions

The Gram-stain-negative, oxidase negative, catalase positive strain KPC-SM-21^T, isolated from a digestate of a storage tank of a mesophilic German biogas plant, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the nearly full-length 16S rRNA gene revealed highest gene sequence similarity to Acinetobacter baumannii ATCC 19606^T (97.0%). Phylogenetic trees calculated based on partial rpoB and gyrB gene sequences showed a distinct clustering of strain KPC-SM-21^T with Acinetobacter gerneri DSM 14967^T = CIP 107464^T and not with A. baumannii, which was also supported in the five housekeeping genes multilocus sequence analysis based phylogeny. Average nucleotide identity values between whole genome sequences of strain KPC-SM-21^T and next related type strains supported the novel species status. The DNA G + C content of strain KPC-SM-21^T was 37.7 mol%. Whole-cell MALDI-TOF MS analysis supported the distinctness of the strain to type strains of next related Acinetobacter species. Predominant fatty acids were C_18:1 ω9c (44.2%), C_16:0 (21.7%) and a summed feature comprising C_16:1 ω7c and/or iso-C_15:0 2-OH (15.3%). Based on the obtained genotypic, phenotypic and chemotaxonomic data we concluded that strain KPC-SM-21^T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter stercoris sp. nov. is proposed. The type strain is KPC-SM-21^T (= DSM 102168^T = LMG 29413^T).

Biologically mediated release of endogenous N2O and NO2 gases in a hydrothermal, hypoxic subterranean environment

The migration of geogenic gases in continental areas with geothermal activity and active faults is an important process releasing greenhouse gases (GHG) to the lower troposphere. In this respect, caves in hypogenic environments are natural laboratories to study the compositional evolution of deep-endogenous fluids through the Critical Zone. Vapour Cave (Alhama, Murcia, Spain) is a hypogenic cave formed by the upwelling of hydrothermal CO₂-rich fluids. Anomalous concentrations of N₂O and NO₂ were registered in the cave's subterranean atmosphere, averaging ten and five times the typical atmospheric backgrounds, respectively. We characterised the thermal conditions, gaseous compositions, sediments, and microbial communities at different depths in the cave. We did so to understand the relation between N-cycling microbial groups and the production and transformation of nitrogenous gases, as well as their coupled evolution with CO₂ and CH₄ during their migration through the Critical Zone to the lower troposphere. Our results showed an evident vertical stratification of selected microbial groups (Archaea and Bacteria) depending on the environmental parameters, including O₂, temperature, and GHG concentration. Both the N₂O isotope ratios and the predicted ecological functions of bacterial and archaeal communities suggest that N₂O and NO₂ emissions mainly depend on the nitrification by ammonia-oxidising microorganisms. Denitrification and abiotic reactions of the reactive intermediates NH₂OH, NO, and NO₂^- are also plausible according to the results of the phylogenetic analyses of the microbial communities. Nitrite-dependent anaerobic methane oxidation by denitrifying methanotrophs of the NC10 phylum was also identified as a post-genetic process during migration of this gas to the surface. To the best of our knowledge, our report provides, for the first time, evidence of a niche densely populated by Micrarchaeia, which represents more than 50% of the total archaeal abundance. This raises many questions on the metabolic behaviour of this and other archaeal phyla.

Acinetobacter lanii sp. nov., Acinetobacter shaoyimingii sp. nov. and Acinetobacter wanghuae sp. nov., isolated from faeces of Equus kiang

Six aerobic, non-motile, non-haemolytic, Gram-stain-negative, oxidase-negative strains (185^T, 187, 323-1^T, 194, dk386^T and dk771) were recovered from different faecal samples of Equus kiang on the Qinghai-Tibet Plateau. In the 16S rRNA gene sequences, one strain pair, 185^T/187, shared highest similarity to Acinetobacter equi 114^T (97.9 %), and the other two (323-1^T/194 and dk771^T/dk386) to Acinetobacter harbinensis CGMCC 1.12528^T (98.6 and 97.0 %, respectively). Phylogenomic tree analysis showed that these six strains formed three separate clades in the genus Acinetobacter. Digital DNA-DNA hybridization values of each pair of the isolates with all members of the genus Acinetobacter were far below 70 %. The main cellular fatty acids of all six strains were C_18 : 1  ω9c, C_16 : 0 and summed feature 3 (C_16 : 1  ω7c/C_16 : 1  ω6c). Q-9 was the predominant respiratory quinone for strains 185^T, 323-1^T and dk386^T. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the genotypic, phenotypic and biochemical analyses, these six strains represent three novel species of the genus Acinetobacter, for which the names Acinetobacter lanii sp. nov., Acinetobacter shaoyimingii sp. nov. and Acinetobacter wanghuae sp. nov. are proposed. The type strains are 185^T (=CGMCC 1.13636^T=JCM 33607^T), 323-1^T (=CGMCC 1.13940^T=JCM 33608^T) and dk386^T (=CGMCC 1.16589^T=JCM 33592^T), respectively.

Assessing the impact of synthetic estrogen on the microbiome of aerated submerged fixed-film reactors simulating tertiary sewage treatment and isolation of estrogen-degrading consortium

17α-ethinylestradiol (EE2) is a synthetic estrogen that can cause harmful effects on animals, such as male feminization and infertility. However, the impact of the EE2 contamination on microbial communities and the potential role of bacterial strains as bioremediation agents are underexplored. The aim of this work was to evaluate the impact of EE2 on the microbial community dynamics of aerated submerged fixed-film reactors (ASFFR) simulating a polishing step downstream of a secondary sewage treatment. For this purpose, the reactors were fed with a synthetic medium with low COD content (around 50 mg l^-1), supplemented (reactor H) or not (reactor C) with 1 μg l^-1 of EE2. Sludge samples were periodically collected during the bioreactors operation to assess the bacterial profile over time by 16S rRNA gene amplicon sequencing or by bacterial isolation using culture-dependent approach. The results revealed that the most abundant phyla in both reactors were Proteobacteria and Bacteroidetes. At genus level, Chitinophagaceae, Nitrosomonas and Bdellovibrio predominated. Significant effects caused by EE2 treatment and bioreactors operating time were observed by non-metric multidimensional scaling. Therefore, even at low concentrations as 1 μg l^-1, EE2 is capable of influencing the bioreactor microbiome. Culture-dependent methods showed that six bacterial isolates, closely related to Pseudomonas and Acinetobacter genera, could grow on EE2 as the sole carbon source under aerobic conditions. These organisms may potentially be used for the assembly of an EE2-degrading bacterial consortium and further exploited for bioremediation applications, including tertiary sewage treatment to remove hormone-related compounds not metabolized in secondary depuration stages.

Pilot-scale study on the effects of cyanobacterial blooms on Vallisneria natans and biofilms at different phosphorus concentrations

Cyanobacterial blooms cause potential risk to submerged macrophytes and biofilms in eutrophic environments. This pilot-scale study investigated the growth, oxidative responses, and detoxification activity of aquatic plants in response to cyanobacterial blooms under different phosphorus concentrations. Variations of extracellular polymeric substances (EPSs) and microbial community composition were also assessed. Results showed that the biomass of Vallisneria natans increased with exposure to cyanobacterial blooms at higher phosphorous concentrations (P > 0.2 mg L^-1). The amount of microcystin compounds (MC-LR) released into the water and the accumulation of MC-LR into both plant tissue and biofilms changed according to the phosphorus concentration. Furthermore, a certain degree of oxidative stress was induced in the plants, as evidenced by increased activity of superoxide dismutase, catalase, and peroxidase, as well as increased malondialdehyde concentrations; significant differences were also seen in acid phosphatase and glutathione S-transferase activities, as well as in glutathione concentrations. Together, these responses indicate potential mechanisms of MC-LR detoxification. Broader α-D-glucopyranose polysaccharides (PS) increased with increasing phosphorous and aggregated into clusters in biofilm EPS in response to the cyanobacterial blooms. In addition, alterations were seen in the abundance and structure of the microbial communities present in exposed biofilms. These results demonstrate that cyanobacterial blooms under different concentrations of phosphorus can induce differential responses, which can have a significant impact on aquatic ecosystems.

Isolation and experimental challenge of cultured burbot (Lota lota maculosa) with Flavobacterium columnare and Aeromonas sp. isolates

Burbot (Lota lota maculosa) are a potential new species for commercial aquaculture. As burbot culture expands, there is a need to further define pathogen susceptibility and characterize aspects of the burbot immune response in an effort to assess fish health. A recent clinical diagnostic case from juvenile burbot reared at a commercial production facility resulted in the isolation and identification of Flavobacterium columnare along with several Aeromonas spp. The F. columnare isolate was assigned to genetic group 1 via multiplex PCR, a genetic group commonly associated with columnaris disease cases in rainbow trout (Oncorhynchus mykiss). Virulence of the F. columnare isolate was assessed in vivo in both juvenile burbot and rainbow trout. Additionally, several of the Aeromonas sp. case isolates were identified via sequencing (16S rRNA, gyrB and rpoD) and a putative A. sobria isolate (BI-3) was used to challenge burbot, along with a known virulent Aeromonas sp. (A141), but BI-3 was not found to be virulent. Burbot were refractory to F. columnare when challenged by immersion, and it is likely that this is a secondary pathogen for burbot. Although refractory in burbot, the identified F. columnare isolate (BI-1) was found to be virulent in rainbow trout.

Non-antibiotic pharmaceuticals enhance the transmission of exogenous antibiotic resistance genes through bacterial transformation

Antibiotic resistance is a serious global threat for public health. Considering the high abundance of cell-free DNA encoding antibiotic resistance genes (ARGs) in both clinical and environmental settings, natural transformation is an important horizontal gene transfer pathway to transmit antibiotic resistance. It is acknowledged that antibiotics are key drivers for disseminating antibiotic resistance, yet the contributions of non-antibiotic pharmaceuticals on transformation of ARGs are overlooked. In this study, we report that some commonly consumed non-antibiotic pharmaceuticals, at clinically and environmentally relevant concentrations, significantly facilitated the spread of antibiotic resistance through the uptake of exogenous ARGs. This included nonsteroidal anti-inflammatories, ibuprofen, naproxen, diclofenac, the lipid-lowering drug, gemfibrozil, and the β-blocker propranolol. Based on the results of flow cytometry, whole-genome RNA sequencing and proteomic analysis, the enhanced transformation of ARGs was affiliated with promoted bacterial competence, enhanced stress levels, over-produced reactive oxygen species and increased cell membrane permeability. In addition, a mathematical model was proposed and calibrated to predict the dynamics of transformation during exposure to non-antibiotic pharmaceuticals. Given the high consumption of non-antibiotic pharmaceuticals, these findings reveal new concerns regarding antibiotic resistance dissemination exacerbated by non-antibiotic pharmaceuticals.

Abundance of mobile genetic elements in an Acinetobacter lwoffii strain isolated from Transylvanian honey sample

Based on phylogenetic analyses, strain M2a isolated from honey, an unexpected source of acinetobacters, was classified as Acinetobacter lwoffii. The genome of this strain is strikingly crowded with mobile genetic elements. It harbours more than 250 IS elements of 15 IS-families, several unit and compound transposons and 15 different plasmids. These IS elements, including 30 newly identified ones, could be classified into at least 53 IS species. Regarding the plasmids, 13 of the 15 belong to the Rep-3 superfamily and only one plasmid, belonging to the “Low-GC” family, possesses a seemingly complete conjugative system. The other plasmids, with one exception, have a mobilization region of common pattern, consisting of the divergent mobA/mobL-family and mobS-, mobC- or traD-like genes separated by an oriT-like sequence. Although two plasmids of M2a are almost identical to those of A. lwoffi strains isolated from gold mine or Pleistocene sediments, most of them have no close relatives. The presence of numerous plasmid-borne and chromosomal metal resistance determinants suggests that M2a previously has also evolved in a metal-polluted environment. The numerous, possibly transferable, plasmids and the outstanding number of transposable elements may reflect the high potential of M2a for rapid evolution.

Response of submerged macrophytes and periphyton biofilm to water flow in eutrophic environment: Plant structural, physicochemical and microbial properties

The integrated effects of water flow on submerged macrophytes (Vallisneria natans) and leaf biofilms were comprehensively investigated in eutrophic microcosm. Changes in aquatic environmental factors were analyzed and water flow was found to elevate eutrophic water quality, especially in terms of TP removal. The removal efficiency of TP reached 78.95% in flowing water, which was more than 10-fold higher than in static water. Water flow altered the morphological and physiological characteristics of plants, decreasing the cell wall thickness and rate of photosynthesis, while promoting the accumulation of soluble sugar and protein in leaves. The starch content also increased with water flow, and significantly larger starch granules were observed in chloroplast. Furthermore, oxidative damage was evidenced by the consistently higher content of malondialdehyde in flowing water. Superoxide dismutase (SOD), peroxidase (POD) and Catalase (CAT) were induced in plants exposed to water flow, as an antioxidant stress response. The results of 16S rRNA high-throughput sequencing analysis showed that the structure of the biofilm microbial community changed in response to water flow. These results expand our understanding of the effects of water flow on submerged macrophytes and periphyton biofilms in eutrophic environments.

Acinetobacter Strain KUO11TH, a Unique Organism Related to Acinetobacter pittii and Isolated from the Skin Mucus of Healthy Bighead Catfish and Its Efficacy Against Several Fish Pathogens

The bacterial strain KU011TH was isolated from the skin mucus of healthy bighead catfish. The strain is a Gram-negative coccobacillus that is nonmotile, aerobic, catalase positive, oxidase negative, and nonhemolytic. Sequence analyses of the housekeeping genes 16S rRNA, gyrB and rpoB indicate that this strain is a new member of the Acb complex of the genus Acinetobacter and is closely related to Acinetobacter pittii and Acinetobacter lactucae. In addition, the genome relatedness-associated ANIb (<95–96%) and in silico DDH (<70%) values clearly supported the new member of the genus Acinetobacter and the Acb complex. The genome of the strain KU011TH was approximately 3.79 Mbp in size, comprising 3619 predicted genes, and the DNA G+C content was 38.56 mol%. The major cellular fatty acids were C18:1ω9c, C16:0, C16:1, C20:2, C18:2ω6c and C18:1ω9t. The whole-genome sequences and phenotypic, phylogenetic, and chemotaxonomic data clearly support the classification of the strain KU011TH as a new member in the genus Acinetobacter which is closest to A. pittii. Additionally, the new bacterial strain exhibited strong activity against a broad range of freshwater fish pathogens in vitro.

Biodegradation of phenol by Acinetobacter tandoii isolated from the gut of the termite

The diet of wood-feeding termites (WFT) consists of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are utilized by symbiotic protozoa as a carbon source. Protozoa produce acetate, which is the carbon source of the termite. Recently, the mechanisms by which lignin is modified by termites have been reported. Lignin is broken down into its phenylpropanoid monomers and phenolic compounds. Bacteria from WFT gut capable of degrading lignin metabolic products are potentially valuable for bioremediation and biofuel production. A bacterium was isolated from the gut of the WFT and identified as Acinetobacter tandoii. This bacterium was capable of utilizing phenol as the sole carbon source and was able to completely degrade phenol at the concentration of 280 mg/L. A. tandoii degraded phenol via the ortho and β-ketoadipase pathway. This bacterium is a known phenol degrader, but to our knowledge, this is the first time it was isolated and tested for phenol-degrading ability from termites.

Bioinformatic Analysis of the Type VI Secretion System and Its Potential Toxins in the Acinetobacter Genus

Several Acinetobacter strains are important nosocomial pathogens, with Acinetobacter baumannii as the species of greatest concern worldwide due to its multi-drug resistance and recent appearance of hyper-virulent strains in the clinical setting. Acinetobacter colonization of the environment and the host is associated with a multitude of factors which remain poorly characterized. Among them, the secretion systems (SS) encoded by Acinetobacter species confer adaptive advantages depending on the niche occupied. Different SS have been characterized in this group of microorganisms, including T6SS used by several Acinetobacter species to outcompete other bacteria and in some A. baumannii strains for Galleria mellonella colonization. Therefore, to better understand the distribution of the T6SS in this genus we carried out an in-depth comparative genomic analysis of the T6SS in 191 sequenced strains. To this end, we analyzed the gene content, sequence similarity, synteny and operon structure of each T6SS loci. The presence of a single conserved T6SS-main cluster (T6SS-1), with two different genetic organizations, was detected in the genomes of several ecologically diverse species. Furthermore, a second main cluster (T6SS-2) was detected in a subgroup of 3 species of environmental origin. Detailed analysis also showed an impressive genetic versatility in T6SS-associated islands, carrying VgrG, PAAR and putative toxin-encoding genes. This in silico study represents the first detailed intra-species comparative analysis of T6SS-associated genes in the Acinetobacter genus, that should contribute to the future experimental characterization of T6SS proteins and effectors.

Analyses of physicochemical properties, bacterial microbiota, and lactic acid bacteria of fresh camel milk collected in Inner Mongolia

Camel milk has significant economic value and is an important food in the region of Alxa Left Banner of Inner Mongolia. Fifteen fresh camel milk samples were collected from domesticated camels in a pasture of Alxa Left Banner. The physicochemical properties and bacterial diversity of camel milk samples were analyzed. The average values of fat, total protein, nonfat milk solids, acidity, and density were 4.40%, 3.87%, 9.50%, 16.95°T, and 1.02 g/cm³, respectively. The bacterial microbiota of the collected fresh camel milk was investigated using PacBio single-molecule real-time (Pacific Biosciences, Menlo Park, CA) sequencing. The camel milk microbiota was highly diverse and comprised 8,513 operational taxonomic units belonging to 32 phyla, 377 genera, and 652 species. The major phyla included Proteobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, and Actinobacteria. A small number of lactic acid bacteria sequences were detected, representing the species Streptococcus thermophilus, Lactobacillus helveticus, Lactococcus lactis, and Leuconostoc mesenteroides. A total of 72 strains of lactic acid bacteria were isolated and identified from 15 samples, including Lactobacillus paracasei, Enterococcus italicus, Enterococcus durans, Lactococcus lactis ssp. lactis, Weissella confusa, and Enterococcus faecium. These results confirm that fresh camel milk has a high bacterial diversity and is a valuable natural resource for isolation of novel lactic acid bacteria.

Carbon ecology of termite gut and phenol degradation by a bacterium isolated from the gut of termite

Metagenomics and transcriptomics have had some success analyzing community and functional ecology of the termite gut, but carbon utilization ecology and the effect of diet on the gut community are not well understood. This study was done to determine the effect of three hardwood tree types, oak (Quercus spp.), red maple (Acer rubrum), and tupelo (Nyssa aquatica) on the termite species, Reticulitermes flavipes in the family Rhinotermitidae. Termite abdomen homogenates were incubated on agar plates containing three common carbon sources in the termite gut, namely, acetate, cellobiose, and phenol under aerobic and anaerobic conditions. Bacterial growth was higher on cellobiose than any other carbon source. Higher bacterial growth on cellobiose was observed from termite colonies feeding on oak than on phenol from the other two wood types. The difference between aerobic and anaerobic conditions was not significant. A bacterium, Acinetobacter tandoii isolated and identified from our previous study was subjected to high concentrations of phenol as the sole carbon source and this bacterium was able to degrade phenol concentration up to 600 mg/L.

The natural environment as a reservoir of pathogenic and non-pathogenic Acinetobacter species

Acinetobacter is a genus of Gram-negative bacteria, which are oxidase-negative, exhibiting a twitching motility under a magnifying lens. Besides being important soil microorganisms, due to their contribution to the soil fertility, Acinetobacter species, particularly A. baumannii, hold a prominent place within the genus because, it is the most virulent among the other species, causing varying degrees of human infections in clinical environments. However, results of different research have shown that Acinetobacter species can be isolated from such natural environments as surface water, wastewater and sewage, healthy human skin, plant, animal and food material as well as domestic appliances. The presence of some other Acinetobacter species in the natural environment has been associated with beneficial roles including soil improvement, detoxification of oil spillages and as microflora in human and plant bodies. In this paper, we carried out an overview of various natural ecological niches as reservoirs of pathogenic and non-pathogenic Acinetobacter species.

Dynamic decoupling of biomass and wax ester biosynthesis in Acinetobacter baylyi by an autonomously regulated switch

For improving the microbial production of fuels and chemicals, gene knock-outs and overexpression are routinely applied to intensify the carbon flow from substrate to product. However, their possibilities in dynamic control of the flux between the biomass and product synthesis are limited, whereas dynamic metabolic switches can be used for optimizing the distribution of carbon and resources. The production of single cell oils is especially challenging, as the synthesis is strictly regulated, competes directly with biomass, and requires defined conditions, such as nitrogen limitation. Here, we engineered a metabolic switch for redirecting carbon flow from biomass to wax ester production in Acinetobacter baylyi ADP1 using acetate as a carbon source. Isocitrate lyase, an essential enzyme for growth on acetate, was expressed under an arabinose inducible promoter. The autonomous downregulation of the expression is based on the gradual oxidation of the arabinose inducer by a glucose dehydrogenase gcd. The depletion of the inducer, occurring simultaneously to acetate consumption, switches the cells from a biomass mode to a lipid synthesis mode, enabling the efficient channelling of carbon to wax esters in a simple batch culture. In the engineered strain, the yield and titer of wax esters were improved by 3.8 and 3.1 folds, respectively, over the control strain. In addition, the engineered strain accumulated wax esters 19% of cell dry weight, being the highest reported among microbes. The study provides important insights into the dynamic engineering of the biomass-dependent synthesis pathways for the improved production of biocompounds from low-cost and sustainable substrates.

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Efficient conversion of acetate to storage lipids (wax ester) is demonstrated.

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AraC-pBAD promoter coupled with glucose dehydrogenase was used as a dynamic switch.

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The autonomous switch allowed dynamic shift from biomass to lipid synthesis mode.

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Wax ester yield and titer were improved by 3–4 folds over the wild type strain.

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The highest amount of wax esters produced in microbes, 19% of CDW, was achieved.

Efficient phosphate accumulation in the newly isolated Acinetobacter junii strain LH4

Phosphate (PO₄^3-) accumulation associated with bacteria contributes to efficient remediation of eutrophic waters and has attracted attention due to its low cost, high removal efficiency and environmental friendliness. In the present study, we isolated six strains from sludge with high concentrations of chemical oxygen demand, total nitrogen and total phosphorus levels. Among them, strain LH4 exhibited the greatest PO₄^3- removal ability. Strain LH4 is typical of Acinetobacter junii based on physiological, biochemical, and molecular analyses and is a PO₄^3--accumulating organism (PAO) based on toluidine blue staining. The strain grew quickly when subjected to aerobic medium after pre-incubation under anaerobic condition, with a maximum OD₆₀₀ of 1.429 after 8 h and PO₄^3- removal efficiency of 99%. Our data also indicated that this strain preferred utilizing the carbon (C) sources sodium formate and sodium acetate and the nitrogen (N) sources NH₄Cl and (NH₄)₂SO₄ over other compounds. To achieve optimal PO₄^3- removal efficiency, a C:N ratio of 5:1, inoculation concentration of 3%, solution pH of 6, incubation temperature of 30 °C, and shaking speed of 100 rpm were recommended for A. junii strain LH4. By incubating this strain with different concentrations of PO₄^3-, we calculated that its relative PO₄^3- removal capacity ranged from 0.67 to 3.84 mg L^-1 h^-1, ranking in the top three among reported PAOs. Our study provided a new PO₄^3--accumulating bacterial strain that holds promise for remediating eutrophic waters, and its potential for large-scale use warrants further investigation.

Field assessment of bacterial communities and total trihalomethanes: Implications for drinking water networks

Operation and maintenance (O&M) of drinking water distribution networks (DWDNs) in tropical countries simultaneously face the control of acute and chronic risks due to the presence of microorganisms and disinfection by-products, respectively. In this study, results from a detailed field characterization of microbiological, chemical and infrastructural parameters of a tropical-climate DWDN are presented. Water physicochemical parameters and the characteristics of the network were assessed to evaluate the relationship between abiotic and microbiological factors and their association with the presence of total trihalomethanes (TTHMs). Illumina sequencing of the bacterial 16s rRNA gene revealed significant differences in the composition of biofilm and planktonic communities. The highly diverse biofilm communities showed the presence of methylotrophic bacteria, which suggest the presence of methyl radicals such as THMs within this habitat. Microbiological parameters correlated with water age, pH, temperature and free residual chlorine. The results from this study are necessary to increase the awareness of O&M practices in DWDNs required to reduce biofilm formation and maintain appropriate microbiological and chemical water quality, in relation to biofilm detachment and DBP formation.

Isolation and characterization of metaldehyde-degrading bacteria from domestic soils

Metaldehyde is a common molluscicide, used to control slugs in agriculture and horticulture. It is resistant to breakdown by current water treatment processes, and its accumulation in drinking water sources leads to regular regulatory failures in drinking water quality. To address this problem, we isolated metaldehyde-degrading microbes from domestic soils. Two distinct bacterial isolates were cultured, that were able to grow prototrophically using metaldehyde as sole carbon and energy source. One isolate belonged to the genus Acinetobacter (strain designation E1) and the other isolate belonged to the genus Variovorax (strain designation E3). Acinetobacter E1 was able to degrade metaldehyde to a residual concentration < 1 nM, whereas closely related Acinetobacter strains were completely unable to degrade metaldehyde. Variovorax E3 grew and degraded metaldehyde more slowly than Acinetobacter E1, and residual metaldehyde remained at the end of growth of the Variovorax E3 strain. Biological degradation of metaldehyde using these bacterial strains or approaches that allow in situ amplification of metaldehyde-degrading bacteria may represent a way forward for dealing with metaldehyde contamination in soils and water.

Transformation of anaerobic granules into aerobic granules and the succession of bacterial community

In this study, we demonstrated that anaerobic granular sludge could be successfully transformed into aerobic granular sludge in a continuous up-flow reactor in 45 days. An aerobic microbial community successfully developed in the granules and high organic matter and nitrogen removal performance was achieved. Under an ammonia nitrogen loading rate of 0.8 kg N/(m³ day), ammonia nitrogen and the total nitrogen removal efficiency of the reactor reached up to 100 and 93%, respectively. An obvious bacterial community shift in granular sludge was observed during the transformation process. By comparing with the bacterial community in aerobic granules cultivated from floccular activated sludge, some bacteria (affiliated with Comamonadaceae, Xanthomonadaceae, Rhodocyclaceae, Moraxellaceae, and Nitrosomonadaceae) playing significant roles in maintaining the structures and functions of aerobic granules were identified. After the transformation, the granules could be clearly separated into the inner core and outer shell. 16S rRNA gene sequencing results indicated many bacterial species present in both the inner core and outer shell; however, their abundance differed significantly. Overall, this study confirms the feasibility of transforming anaerobic granules into aerobic granules and provides novel approaches and insights to understand the microbial ecology in granular sludge.

Genomic and physiological characterization of a laboratory-isolated Acinetobacter schindleri ACE strain that quickly and efficiently catabolizes acetate

An Acinetobacter strain, designated ACE, was isolated in the laboratory. Phylogenetic tests and average nucleotide identity value comparisons suggested that ACE belongs to the species Acinetobacterschindleri. We report for the first time the complete genome sequence of an A. schindleri strain, which consists of a single circular chromosome of 3 001 209 bp with an overall DNA G+C content of 42.9 mol% and six plasmids that account for 266 844 bp of extrachromosomal material. The presence or absence of genes related to carbon catabolism and antibiotic resistance were in agreement with the phenotypic characterization of ACE. This strain grew faster and with a higher biomass yield on acetate than the reference strain Acinetobacter baylyi ADP1. However, ACE did not use aromatic compounds and was unable to grow on common carbon sources, such as glucose, xylose, glycerol or citrate. The gluconeogenic and the catechol pathways are complete in ACE, but compounds that are converted to protocatechuate did not sustain growth since some genes of this pathway are missing. Likewise, this strain could not grow on glucose because it lacks the genes of the Entner-Doudoroff pathway. Minimal inhibitory concentration data showed that ACE was susceptible to most of the antimicrobial agents recommended for the clinical treatment of Acinetobacter spp. Some genes related to a possible human-microbe interaction were found in the ACE genome. ACE is likely to have a low pathogenic risk, as is the case with other A. schindleri strains. These results provide a valuable reference for broadening the knowledge of the biology of Acinetobacter.

Acinetobacter defluvii sp. nov., recovered from hospital sewage

A Gram-stain-negative, non-motile Acinetobacter strain, WCHA30T, was isolated from hospital sewage in West China Hospital of Sichuan University in Chengdu, south-western China. Strain WCHA30T was a non-spore-forming, catalase-positive, oxidase-negative, strictly aerobic coccobacillus. The DNA G+C content was 38 mol%. Phylogenetic analysis based on 16S rRNA, rpoB and gyrB gene sequences revealed that the strain was distinct from any previously described species of the genus Acinetobacter. Strain WCHA30T could be distinguished from all known Acinetobacter species by its ability to assimilate β-alanine but not l-glutamate. Genotypic and phenotypic characteristics from this study indicate that strain WCHA30T should be considered to represent a novel species of the genus Acinetobacter, for which the name Acinetobacter defluvii sp. nov. is proposed. The type strain is WCHA30T (=CCTCC AB 2016203T=GDMCC 1.1101T=KCTC 52503T).