Genus Acinetobacter Research Articles

Current to Biomass: Media Optimization and Strain Selection from Cathode-Associated Microbial Communities in a Two-Chamber Electro-Cultivation Reactor

Cathode-associated microbial communities (caMCs) are the functional key elements in the conversion of excess electrical energy into biomass. In this study, we investigated the development of electrochemical caMCs based on two-chamber microbial electrolytic cells (MECs) after optimization of media composition. Microbial communities obtained from a historical soil sample were inoculated into the cathode chamber of MECs. The inorganic medium with (A) carbon dioxide in air or (B) 100 mM sodium bicarbonate as carbon source was used in the absence of any organic carbon source. After 12 days of operation, the experimental results showed that (1) the bacterial community in group B exhibited lush growth and (2) a single strain TX168 Epilithonimonas bovis isolated from group A indicated electrochemical activity and synthesized large volumes of biomass using sodium bicarbonate. We also analyzed the caMCs of the MECs and reference samples without electro-cultivation using 16S rRNA gene sequencing. The results showed that the caMCs of MECs in groups A and B were dominated by the genera Acinetobacter and Pseudomonas. The caMCs were further inoculated and cultured on different agars to isolate specific electroactive bacterial strains. Overall, our study highlights the possibility of converting excess energy into biomass by electro-cultivation and the importance of selecting appropriate media to enrich specific microbial communities and single strains in MECs.

The problem of methicillin-resistant Staphylococcus and Acinetobacter nosocomial infections (Literature review)

Sosocomial septic infections continue to remain one of the leading causes of mortality in hospital wards. In this context, nosocomial infections caused by novel aetiological agents of the Staphylococcus and Acinetobacter genera are a current problem. The article presents relevant data on the topic of the spread of nosocomial infections with methicillin-resistant Staphylococcus and Acinetobacter worldwide, as well as the situation regarding the spread of these infections in the Republic of Moldova.

Genomic and phenotypic features of Acinetobacter baumannii isolated from oil reservoirs reveal a novel subspecies specialized in degrading hazardous hydrocarbons

The genus Acinetobacter encompasses biotechnologically relevant species and nosocomial pathogens. In this study, nine isolates recovered from different oil reservoir samples showed the ability to grow with petroleum as the only carbon source and possessed the ability to emulsify kerosene. The whole genomes of the nine strains were sequenced and analyzed. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of all strains were compared to the reference strains, and the results were below the reference values (<97.88 and 82, respectively), suggesting that the isolates belong to a new subspecies of Acinetobacter baumannii. The name Acinetobacter baumannii oleum ficedula is proposed. A comparison of the whole genome repertoire of 290 Acinetobacter species indicated that the strains in this study resemble non-pathogenic Acinetobacter strains. However, the new isolates resemble A. baumannii when comparing virulence factors. The isolates in this study carry many genes involved in hydrocarbon degradation, indicating the potential to degrade most toxic compounds listed by environmental regulatory agencies such as ATSDR, EPA, and CONAMA. In addition, despite the absence of known biosurfactant or bioemulsifier genes, the strains showed emulsifying activity, suggesting the presence of new pathways or genes related to this process. This study investigated the genomic, phenotypic, and biochemical features of the novel environmental subspecies A. baumannii oleum ficedula, revealing their potential to degrade hydrocarbons and to produce biosurfactants or bioemulsifiers. Applying these environmental subspecies in bioaugmentation strategies sheds light on future approaches to bioremediation. The study shows the importance of genomic analysis of environmental strains and their inclusion in metabolic pathways databases, highlighting unique enzymes/alternative pathways for consuming hazardous hydrocarbons.

Bacterioplankton Communities in Dissolved Organic Carbon-Rich Amazonian Black Water.

The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear, and black waters. In black water, important loads of allochthonous humic dissolved organic matter (DOM) result from the bacterioplankton degradation of plant lignin. However, the bacterial taxa involved in this process remain unknown, since Amazonian bacterioplankton has been poorly studied. Its characterization could lead to a better understanding of the carbon cycle in one of the Earth's most productive hydrological systems. Our study characterized the taxonomic structure and functions of Amazonian bacterioplankton to better understand the interplay between this community and humic DOM. We conducted a field sampling campaign comprising 15 sites distributed across the three main Amazonian water types (representing a gradient of humic DOM), and a 16S rRNA metabarcoding analysis based on bacterioplankton DNA and RNA extracts. Bacterioplankton functions were inferred using 16S rRNA data in combination with a tailored functional database from 90 Amazonian basin shotgun metagenomes from the literature. We discovered that the relative abundances of fluorescent DOM fractions (humic-, fulvic-, and protein-like) were major drivers of bacterioplankton structure. We identified 36 genera for which the relative abundance was significantly correlated with humic DOM. The strongest correlations were found in the Polynucleobacter, Methylobacterium, and Acinetobacter genera, three low abundant but omnipresent taxa that possessed several genes involved in the main steps of the β-aryl ether enzymatic degradation pathway of diaryl humic DOM residues. Overall, this study identified key taxa with DOM degradation genomic potential, the involvement of which in allochthonous Amazonian carbon transformation and sequestration merits further investigation. IMPORTANCE The Amazon basin discharge carries an important load of terrestrially derived dissolved organic matter (DOM) to the ocean. The bacterioplankton from this basin potentially plays important roles in transforming this allochthonous carbon, which has consequences on marine primary productivity and global carbon sequestration. However, the structure and function of Amazonian bacterioplanktonic communities remain poorly studied, and their interactions with DOM are unresolved. In this study, we (i) sampled bacterioplankton in all the main Amazon tributaries, (ii) combined information from the taxonomic structure and functional repertory of Amazonian bacterioplankton communities to understand their dynamics, (iii) identified the main physicochemical parameters shaping bacterioplanktonic communities among a set of >30 measured environmental parameters, and (iv) characterized how bacterioplankton structure varies according to the relative abundance of humic compounds, a by-product from the bacterial degradation process of allochthonous DOM.

Regulating aeration intensity to simultaneously improve humification and mitigate gaseous emissions in food waste digestate composting: Performance and bacterial dynamics

This study assessed the impact of aeration intensity on food waste digestate composting to simultaneously govern organic humification and gaseous emissions. Results show that an augment in the aeration intensity from 0.1 to 0.4 L·kg−1 DM·min−1 provided more oxygen to facilitate organic consumption and thus temperature increase, but slightly restrained organic humification (e.g. less humus content and higher E4/E6 ratio) and substrate maturity (i.e. lower germination index). Furthermore, increasing aeration intensity inhibited the proliferation of the genera Tepidimicrobium and Caldicoprobacter to alleviate methane emission and enriched the genus Atopobium to boost hydrogen sulphide production. More importantly, increasing aeration intensity limited the growth of the genus Acinetobacter for nitrite/nitrogen respiration, but strengthened aerodynamics to blow out nitrous oxide and ammonia produced inside piles. Principal component analysis comprehensively indicated that a low aeration intensity of 0.1 L·kg−1DM·min−1 facilitated precursors synthesis toward humus and simultaneously mitigated gaseous emissions to improve food waste digestate composting.

The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate.

Acinetobacter baumannii is an important opportunistic pathogen known for its high levels of resistance to many antibiotics, particularly those considered last resorts such as colistin and carbapenems. Plasmids of this organism are increasingly associated with the spread of clinically important antibiotic resistance genes. Although A. baumannii is a ubiquitous organism, to date, most of the focus has been on studying strains recovered from clinical samples ignoring those isolated in the environment (soil, water, food, etc.). Here, we analysed the genetic structures of eight novel plasmids carried by an environmental colistin-resistant A. baumannii (strain E-072658) recovered in a recycled fibre pulp in a paper mill in Finland. It was shown that E-072658 carries a new variant of the mcr-4 colistin resistance gene (mcr-4.7) in a novel Tn3-family transposon (called Tn6926) carried by a novel plasmid p8E072658. E-072658 is also resistant to sulphonamide compounds; consistent with this, the sul2 sulphonamide resistance gene was found in a pdif module. E-072658 also carries six additional plasmids with no antibiotic resistance genes, but they contained several pdif modules shared with plasmids carried by clinical strains. Detailed analysis of the genetic structure of all eight plasmids carried by E-072658 showed a complex evolutionary history revealing genetic exchange events within the genus Acinetobacter beyond the clinical or environmental origin of the strains. This work provides evidence that environmental strains might act as a source for some of the clinically significant antibiotic resistance genes.

Identification of an Acinetobacter lwoffii strain isolated from diseased hybrid sturgeon (Acipenser baerii♀× Acipenser schrenckii♂)

Members of the genus Acinetobacter are important opportunistic pathogens responsible for various nosocomial infections. However, Acinetobacter spp. are rarely isolated from fish. In this study, we isolated a dominant bacterial strain named I-702 from diseased hybrid sturgeons (Acipenser baerii♀ × Acipenser schrenckii♂) bred at a farm in Yichang City, Hubei Province, China. We identified the strain as Acinetobacter lwoffii based on morphological, physiological and biochemical, and 16S rRNA gene sequence analyses. Regression infection experiments using strain I-702 showed that the symptoms of the artificially infected fish were the same as those of natural diseased sturgeons, such as abdominal congestion and redness and swelling of cloaca. We calculated that the median lethal dose (LD50) of strain I-702 for hybrid sturgeons was 1.22 × 102 ± 0.11 colony forming units/g fish. We also compared the proportion of different leukocytes between healthy and diseased fish; the proportion of neutrophils (30.89%) and monocytes (36.68%) in infected fish increased significantly, whereas that of lymphocytes (30.17%) decreased. Histopathological examination revealed that strain I-702 caused damage to the liver, and intestine tissues of sturgeons. Gut microbial analysis revealed that I-702 infection caused dysbiosis in sturgeons. The relative abundance of Acinetobacter in the diseased group (54.4%) was significantly higher than that in the healthy group (10.7%), whereas the relative abundance of Cetobacterium decreased significantly (healthy sturgeon: 25.6%, diseased sturgeon: 1.5%). Strain I-702 was susceptible to aminoglycosides (neomycin sulfate, amikacin, and gentamycin) and tetracyclines (minocycline and doxycycline). These results suggest that A. lwoffii is an important pathogen of sturgeons. Moreover, the study provides a scientific basis for the control and prevention of A. lwoffii infection in fish.

Global Epidemiology and Mechanisms of Resistance of Acinetobacter baumannii-calcoaceticus Complex.

Acinetobacter baumannii-calcoaceticus complex is the most commonly identified species in the genus Acinetobacter and it accounts for a large percentage of nosocomial infections, including bacteremia, pneumonia, and infections of the skin and urinary tract. A few key clones of A. baumannii-calcoaceticus are currently responsible for the dissemination of these organisms worldwide. Unfortunately, multidrug resistance is a common trait among these clones due to their unrivalled adaptive nature. A. baumannii-calcoaceticus isolates can accumulate resistance traits by a plethora of mechanisms, including horizontal gene transfer, natural transformation, acquisition of mutations, and mobilization of genetic elements that modulate expression of intrinsic and acquired genes.

AquaSens: exploring the use of 16S rRNA next-generation sequencing to determine bacterial composition of various water matrices

Access to clean water, one of the United Nation’s Sustainable Development Goals, is challenged by an increase in the presence of emerging microbial and other contaminants due to urbanization, among other factors. Traditionally, the presence of indicator microorganisms is determined using culturing methods. However, these classical methods cannot be used to determine the identities of ‘unknown’ bacteria and is limited to isolating the culturable state of microorganisms. Thus with culturing, the identities of many bacteria, particularly novel or non-culturable, may remain unknown. The use of a DNA-based method, 16S rRNA next-generation sequencing (NGS), can assist with determining the identities of bacterial populations in a water sample. The objective of this 16S rRNA NGS study was to investigate the bacterial community composition and diversity in a range of water sources. Water samples comprising of potable, surface, ground, marine, aquaculture, rain, wetland and swimming bath water matrices were subjected to 16S rRNA NGS using the Illumina 16S rRNA Metagenomics analysis pipeline. Operational taxonomic units were analysed and the identities of bacterial genera determined. In this study, genera of Acinetobacter, Mycobacterium, Pseudomonas, Legionella, Burkholderia, Yersinia, Staphylococcus and Vibrio were spread across the water matrices. Alpha (within sample) and beta (between samples) diversities for each bacterial community within the tested samples were also determined.

Phosphorus biorecovery from wastewater contaminated with multiple nitrogen species by a bacterial consortium

Recovering finite and non-substitutable phosphorus from liquid waste streams through bio-mediated techniques has attracted increasing interest, but current approaches are incredibly dependent on ammonium. Herein, a process to recover phosphorus from wastewater under multiple nitrogen species conditions was developed. This study compared the effects of nitrogen species on the recovery of phosphorus resources by a bacterial consortium. It found that the consortium could not only efficiently utilize ammonium to enable phosphorus recovery but also utilize nitrate via dissimilatory nitrate reduction to ammonium (DNRA) to recover phosphorus. The characteristics of the generated phosphorus-bearing minerals, including magnesium phosphate and struvite, were evaluated. Furthermore, nitrogen loading positively influenced the stability of the bacterial community structure. The genus Acinetobacter was dominant under nitrate and ammonium conditions, with a relatively stable abundance of 89.01% and 88.54%, respectively. The finding may provide new insights into nutrient biorecovery from phosphorus-containing wastewater contaminated with multiple nitrogen species.

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.

Remediation of petroleum contaminated soil by persulfate oxidation coupled with microbial degradation

This study was conducted on soil polluted with high concentrations of crude oil (12,835 ± 572.76 mg/kg) with different dosages of persulfate (PS) coupled with hydrocarbon-degrading mixed bacteria (including Enterobacteriaceae, Stenotrophomonas, Pseudomonas, Acinetobacter, and Achromobacter) obtained from long-term oil-contaminated soil. The interaction among total petroleum hydrocarbons (TPH), soil parameters, and microbial communities during a 187-d combined remediation process was evaluated. The result showed that the TPH removal of 1% PS oxidation combined with bioremediation was 80.05%; this was 4.88% and 20.94% higher than that of bioremediation and 1% PS oxidation combined with natural attenuation. This is a result of 1%PS stimulated enzyme secretion and dissolved organic carbon content, especially fulvic acid, improving TPH mobility and bioavailability in soil. Furthermore, introducing mixed bacteria after oxidation further increased enzyme activities and TPH-degrading ability, thus promoting carbon substrate conversion and biodegradation rate. Conversely, the excessive oxidation of 3% and 5% PS had a negative impact on the soil environment and microbial diversity resulting in lower TPH degradation (36%-57%). High-throughput sequencing revealed that the abundance and diversity of soil bacteria decreased in all remediation groups compared to those in the pristine soil. Redundancy analysis showed that the main factors affecting 1% PS oxidation combined with bioremediation during subsequent microbial remediation were pH, cation exchange capacity, and lipase activity, which may indirectly influence TPH biodegradation by increasing the abundance of genus Immundisolibacteraceae, Comamonadaceae, and Acinetobacter. This study provides data on in situ chemical oxidation integrated with the bioremediation of petroleum hydrocarbon-contaminated soils.

Effects of Microplastic Exposure on the Community Structure and Function of Symbiotic Bacteria in Sinularia microclavata

Microplastics are widely distributed in the marine environment and are harmful to the health of marine organisms (including corals). However, studies on the impact of microplastics on coral have been very limited, and the specific mechanism of their impact is not clear. Therefore, in this study, microplastic PA, which is common in the marine environment, was selected to conduct a 7-day microplastic exposure experiment on Sinularia microclavata. The effects of microplastic exposure at different times on the diversity, community structure, and function of the symbiotic bacterial community of coral were analyzed using high-throughput sequencing technology. The α-diversity of the symbiotic bacterial community of coral first decreased and then increased with the exposure time of microplastics. The analysis of β-diversity and microbial community composition showed that microplastic exposure caused significant changes in the symbiotic bacterial community of coral, and the bacterial community composition also changed with the exposure time. A total of 49 phyla, 152 classes, 363 orders, 634 families, and 1390 genera were detected. At the phylum level, Proteobacteria was the dominant taxa in all samples, but the relative abundance varied among samples. Microplastic exposure increased the abundance of Proteobacteria, Chloroflexi, Firmicutes, Actinobacteriota, Bacteroidota, and Acidobacteriota. At the genus level, Ralstonia, Acinetobacter, and Delftia were the dominant taxa of symbiotic bacteria of coral after microplastic exposure. PICRUSt functional prediction indicated that functions of the coral symbiotic bacterial community, including signal transduction, cellular community prokaryotes, xenobiotics biodegradation and metabolism, and cell motility, decreased after microplastic exposure on coral. BugBase phenotype predictions indicated that microplastic exposure altered three phenotypes (pathogenic, anaerobic, and oxidative stress-tolerant) of the coral symbiotic bacterial community. FAPROTAX functional predictions indicated that microplastic exposure caused significant changes in functions such as the symbiotic relationship between coral symbiotic bacteria and the host, carbon and nitrogen cycling, and photosynthesis. This study provided basic data on the mechanism of microplastic impacts on corals and microplastics ecotoxicology.

Response of the Pardosa astrigera bacterial community to Cry1B protein

While genetically modified (GM) crops bring economic benefits to human beings, their impact on non-target organisms has become an important part of environmental safety assessments. Symbiotic bacteria play an important role in eukaryotic biological functions and can adjust host communities to adapt to new environments. Therefore, this study examined the effects of Cry1B protein on the growth and development of non-target natural enemies of Pardosa astrigera (L. Koch) from the perspective of symbiotic bacteria. Cry1B protein had no significant effect on the health indicators of P. astrigera (adults and 2nd instar spiderlings). 16S rRNA sequencing results revealed that Cry1B protein did not change the symbiotic bacteria species composition of P. astrigera, but did reduce the number of OTU and species diversity. In 2nd instar spiderlings, neither the dominant phylum (Proteobacteria) nor the dominant genus (Acinetobacter) changed, but the relative abundance of Corynebacterium-1 decreased significantly; in adult spiders, the dominant bacteria genera of females and males were different. The dominant bacterial genera were Brevibacterium in females and Corynebacterium-1 in males, but Corynebacterium-1 was the dominant bacteria in both females and males feeding on Cry1B. The relative abundance of Wolbachia also increased significantly. In addition, bacteria in other genera varied significantly by sex. KEGG results showed that Cry1B protein only altered the significant enrichment of metabolic pathways in female spiders. In conclusion, the effects of Cry1B protein on symbiotic bacteria vary by growth and development stage and sex.

Abstract 5909: Characterization of the lung cancer microbiome using whole genome sequencing

Abstract Microbiome studies have been rapidly increasing over the last decade, providing valuable insights into the commensal bacterial contribution to human physiology and disease, including human cancer. Many studies have demonstrated the important roles of the microbiome in cancer progression, anti-tumor immunity, resistance to therapies, metastasis formation, and in some rare cases even cancer development through the production of genotoxins. However, relatively few studies have analyzed the lung cancer microbiome, and both its composition and role in cancer progression are largely unknown. To characterize the microbiome of tumor and matched normal lung tissues, we performed whole-genome sequencing (WGS) in 872 never smokers using the Kraken pipeline. At the phylum level, WGS analyses of tumor and normal samples showed predominantly Proteobacteria and Actinobacteria (58% and 32%, respectively). Notably, we found overall similar microbiome composition in tumor and normal lung tissue samples. At the genus level, Cutibacterium, Klebsiella, Pseudomonas, Sphingomonas, Staphylococcus, and Acinetobacter genera were among the most abundant bacteria in tumor and normal tissues, alike, and the genera Prevotella, Corynebacterium, and Streptococcus were more abundant in tumor samples compared to normal lung tissue. Comparison of alpha diversity at the genus level between tumors and normal samples showed no substantial difference. We are currently investigating whether the microbiome composition varies by lung tumor anatomical location, sex, histology, study subjects’ geographical location, and immune microenvironment. We will also investigate whether the tumor microbiome composition varies in relation to important genomic features, like cancer driver genes and mutational signatures. Finally, we have 16s rRNA seq data from 771 tumor and normal lung tissues from never smokers and we will compare bacterial microbiome composition and diversity based on WGS and 16s rRNA seq for the same samples. This study, based on the largest analysis of lung microbiome to date, is poised to provide important insights into the role of commensal microbiota in shaping lung tumor development and progression. Citation Format: John McElderry, Tongwu Zhang, Jianxin Shi, Maria Teresa Landi. Characterization of the lung cancer microbiome using whole genome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5909.

Vaginal Infections during Pregnancy Increase Breast Milk Microbiome Alpha Diversity and Alter Taxonomic Composition.

We previously reported that breast milk from women with (W) or without (WO) vaginal yeast infection during pregnancy differs in its immunological and antimicrobial properties, especially against pathogenic vaginal Candida sp.. Here, we investigated the differences in microbiota profiles of breast milk from these groups. Seventy-two breast milk samples were collected from lactating mothers (W, n=37; WO, n=35). The DNA of bacteria was extracted from each breast milk sample for microbiota profiling by 16S rRNA gene sequencing. Breast milk from the W-group exhibited higher alpha diversity than that from the WO-group across different taxonomic levels of class (P=0.015), order (P=0.011), family (P=0.020), and genus (P=0.030). Compositional differences between groups as determined via beta diversity showed marginal differences at taxonomic levels of phylum (P=0.087), family (P=0.064), and genus (P=0.067). The W-group showed higher abundances of families Moraxellaceae (P=0.010) and Xanthomonadaceae (P=0.008), and their genera Acinetobacter (P=0.015), Enhydrobacter (P=0.015), and Stenotrophomonas (P=0.007). Meanwhile, the WO-group showed higher abundances of genus Staphylococcus (P=0.046) and species Streptococcus infantis (P=0.025). This study shows that, although breast milk composition is affected by vaginal infection during pregnancy, this may not pose a threat to infant growth and development.

RND pumps across the genus Acinetobacter: AdeIJK is the universal efflux pump.

Acinetobacter are generally soil-dwelling organisms that can also cause serious human infections. A. baumannii is one of the most common causative agents of Acinetobacter infections and is often multidrug resistant. However, an additional 25 species within the genus have also been associated with infection. A. baumannii encodes six resistance nodulation division (RND) efflux pumps, the most clinically relevant class of efflux pumps for antibiotic export, but the distribution and types of RND efflux pumps across the genus is currently unknown. Sixty-four species making up the genus Acinetobacter were searched for RND systems within their genomes. We also developed a novel method using conserved RND residues to predict the total number of RND proteins including currently undescribed RND pump proteins. The total number of RND proteins differed both within a species and across the genus. Species associated with infection tended to encode more pumps. AdeIJK/AdeXYZ was found in all searched species of Acinetobacter, and through genomic, structural and phenotypic work we show that these genes are actually homologues of the same system. This interpretation is further supported by structural analysis of the potential drug-binding determinants of the associated RND-transporters, which reveal their close similarity to each other, and distinctiveness from other RND-pumps in Acinetobacter, such as AdeB. Therefore, we conclude that AdeIJK is the fundamental RND system for species in the genus Acinetobacter. AdeIJK can export a broad range of antibiotics and provides crucial functions within the cell, for example lipid modulation of the cell membrane, and therefore it is likely that all Acinetobacter require AdeIJK for survival and homeostasis. In contrast, additional RND systems, such as AdeABC and AdeFGH, were only found in a subset of Acinetobacter that are associated with infection. By understanding the roles and mechanisms of RND efflux systems in Acinetobacter, treatments for infections can avoid efflux-mediated resistance and improve patient outcomes.

Effects of poultry by-product meal replacing fish meal on growth performance, feed utilization, intestinal morphology and microbiota communities in juvenile large yellow croaker (Larimichthys crocea)

An 8 weeks feeding trail was conducted to evaluate the potential of poultry by-product meal (PBM) replacing fish meal (FM) in the diet of juvenile large yellow croaker (Larimichthys crocea). Five iso-nitrogenous (45% crude protein), iso-lipidic (10% crude lipid) and iso-energetic (about kcal 400 g diet −1) diets were formulated with 0, 25%, 50% 75% and 100% FM being replaced by PBM (marked as FM, PBM25, PBM50, PBM75 and PBM100). Crystal methionine and lysine were added into PBM-containing diets to match its concentration in FM diet. Each diet was randomly assigned to triplicate groups of 30 fish (initial weight 18.43 ± 1.28 g) in floating sea cages. The weight gain, specific growth rate and feed efficiency of L. crocea decreased significantly when the replacement level of FM was higher than 25%. The feed intake of fish fed PBM100 was significantly lower than those fed FM, PBM25 and PBM50. Juveniles fed PBM-containing diets showed significantly lower value of muscular thickness in intestine when compared to those fed FM. Villi length decreased significantly when the replacement of FM in diets was more than 50%. Fish fed FM diet had the relative higher abundances of Exiguobacterium (from order to genus), Bacillus (from order to genus), Pseudomonadales (from order to genus) and Acinetobacter genus, those fed PBM25, PBM50 and/or PBM75 showed higher abundance of Peptostreptococcaceae and Vibrio. Overall, PBM replacing dietary FM may inhibit growth performance of L. crocea through reducing digestibility via declining the abundance of intestinal bacteria that producing digestive enzyme, and improving the abundance of pathogen. Peptostreptococcaceae and Vibrio could be the indicator in the intestinal of L. crocea fed high PBM diets. The optimum dietary FM replacement level by PBM was 25% for L. crocea.

Isolation and characterization of an As(III) oxidizing bacterium, Acinetobacter sp. TMKU4 from paddy field for possible arsenic decontamination

During past few decades arsenic (As), a poisonous and carcinogenic water and soil contaminant, is perceived as a significant universal environmental snag. The exploration of As-resistant microorganisms for mitigation of As-contaminated environment has been proven to be both economical and ecologically favourable among the various techniques so far documented. Several As-resistant bacterial isolates were isolated from the soil sample of As affected area of Nadia, a district in West Bengal, India. On the basis of maximum As resistance ability, an arsenite [As(III)]-oxidizing bacterial strain, TMKU4, was selected, which could withstand 12.5 mM As(III) and 95 mM arsenate [As(V)]. The strain was noted to be closely linked to the genus Acinetobacter as per 16S rDNA sequence analysis and biochemical characterization. Within 14 h of incubation on minimal salts medium, this strain could convert ∼78% of As(III) to As(V). Kinetic evaluation of partially purified As(III) oxidase from the bacterial cells exhibited Km of 73.38 μM and Vmax of 0.3456 μM min−1 μg−1 protein. The existence of the As(III) oxidase gene was further confirmed through PCR with degenerate primers. TMKU4 exhibits potential plant growth-promoting attributes owing to which it could also be exploited as a promising As bioremediation strategy for sustainable agriculture.

Effects of Sulfamethoxazole and Florfenicol on Growth, Antioxidant Capacity, Immune Responses and Intestinal Microbiota in Pacific White Shrimp Litopenaeus vannamei at Low Salinity.

Antibiotic residue may pose a serious risk to aquaculture, and the culture of Litopenaeus vannamei in a low-salinity environment is a growing trend over the world. Here, we aimed to understand the combined effect of low salinity and sulfamethoxazole (SMZ) and florfenicol (FLO) antibiotics on L. vannamei. The growth performance, immune functions, antioxidant capacity and intestinal microbiota were investigated. Compared with the control group, the weight gain and survival rate significantly decreased (p < 0.05) in shrimp after they were exposed to low-salinity (salinity 3) water and the mixture of antibiotics and low-salt conditions for 28 days. The antioxidant activities of SOD and T-AOC, shown at low salinity and in the higher concentration of the SMZ treatment group (SMZH), were significantly decreased, while the GST activity was significantly increased in each treatment group in comparison with the control group. The expression of immune-related genes, including TOLL, LvIMD, PPO and HSP, in the low concentration of the SMZ treatment group (SMZL) was higher than that in the other groups. The diversity of intestine microbiota was disturbed with a lower Shannon index in the low-salinity and SMZH groups, and a higher Simpson index in the SMZH group. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant phyla in the gut of L. vannamei. At the genus level, Microbacterium, Shewanella, Aeromonas, Acinetobacter, Gemmobacter, Paracoccus and Lysobacter were significantly decreased in the low-salinity group. However, the abundance of opportunistic pathogens belonging to the genus Aeromonas in the FLO group was increased. The predicted microbe-mediated functions showed that the pathway for "amino acid metabolism" and "replication and repair" was significantly inhibited in both the low-salinity and antibiotic-exposed groups. All the findings in this study indicate that the combined effect of antibiotics and low salinity on L. vannamei negatively impacted the physiological and intestinal microbiota functions.