Prioritization of Mur family drug targets against A. baumannii and identification of their homologous proteins through molecular phylogeny, primary sequence, and structural analysis

Background

The World Health Organization (WHO) report stated that Acinetobacter baumannii had been classified as one of the most important pathogenic bacteria causing nosocomial infection in hospital patients due to multi-drug resistance (MDR). It is vital to find out new bacterial drug targets and annotated their structure and function for the exploration of new anti-bacterial agents. The present study utilized a systematic route to prioritize the potential drug targets that belong to Mur family of Acinetobacter baumannii and identify their homologous proteins using a computational approach such as sequence similarity search, multiple sequence alignment, phylogenetic analysis, protein sequence, and protein structure analysis.

Results

From the results of protein sequence analysis of eight Mur family proteins, they divided into three main enzymatic classes namely transferases (MurG, MurA and MraY), ligases (MurC, MurD, MurE, and MurF), and oxidoreductase (MurB). Based on the results of intra-comparative protein sequence analysis and enzymatic classification, we have chosen MurB, MurE, and MurG as the prioritized drug targets from A. baumannii and subjected them for further detailed studies of inter-species comparison. This inter-species comparison help us to explore the sequential and structural properties of homologous proteins in other species and hence, opens a gateway for new target identification and using common inhibitor for different bacterial species caused by various diseases. The pairwise sequence alignment results between A. baumannii’s MurB with A. calcoaceticus’s MurB, A. baumannii’s MurE with A. seifertii’s MurE, and A. baumannii’s MurG with A. pittii’s MurG showed that every group of the proteins are highly similar with each other and they showed sequence identity of 95.7% and sequence similarity of 97.2%.

Conclusion

Together with the results of secondary and three-dimensional structure predictions explained that three selected proteins (MurB, MurE, and MurG) from A. baumannii and their related proteins (AcMurB, AsMurE, and ApMurG) belong to mixed αβ class and they are very similar.

The occurrence of Salmonella, extended-spectrum β-lactamase producing Escherichia coli and carbapenem resistant non-fermenting Gram-negative bacteria in a backyard poultry flock environment

Increase in the number of small-scale backyard poultry flocks in the USA has substantially increased human-to-live poultry contact, leading to increased public health risks of the transmission of multi-drug resistant (MDR) zoonotic and food-borne bacteria. The objective of this study was to detect the occurrence of Salmonella and MDR Gram-negative bacteria (GNB) in the backyard poultry flock environment. A total of 34 backyard poultry flocks in Washington State (WA) were sampled. From each flock, one composite coop sample and three drag swabs from nest floor, waterer-feeder, and a random site with visible faecal smearing, respectively, were collected. The samples were processed for isolation of Salmonella and other fermenting and non-fermenting GNB under ceftiofur selection. Each isolate was identified to species level using MALDI-TOFF and tested for resistance against 16 antibiotics belonging to eight antibiotic classes. Salmonella serovar 1,4,[5],12:i:- was isolated from one (3%) out of 34 flocks. Additionally, a total of 133 ceftiofur resistant (Cef^R ) GNB including Escherichia coli (53), Acinetobacter spp. (45), Pseudomonas spp. (22), Achromobacter spp. (8), Bordetella trematum (1), Hafnia alvei (1), Ochrobactrum intermedium (1), Raoultella ornithinolytica (1), and Stenotrophomonas maltophilia (1) were isolated. Of these, 110 (82%) isolates displayed MDR. Each flock was found positive for the presence of one or more Cef^R GNB. Several MDR E. coli (n = 15) were identified as extended-spectrum β-lactamase (ESBL) positive. Carbapenem resistance was detected in non-fermenting GNB including Acinetobacter spp. (n = 20), Pseudomonas spp. (n = 11) and Stenotrophomonas maltophila (n = 1). ESBL positive E. coli and carbapenem resistant non-fermenting GNB are widespread in the backyard poultry flock environment in WA State. These GNB are known to cause opportunistic infections, especially in immunocompromised hosts. Better understanding of the ecology and epidemiology of these GNB in the backyard poultry flock settings is needed to identify potential risks of transmission to people in proximity.

Chromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus

Acinetobacter haemolyticus is a Gammaproteobacterium that has been involved in serious diseases frequently linked to the nosocomial environment. Most of the strains causing such infections are sensitive to a wide variety of antibiotics, but recent reports indicate that this pathogen is acquiring very efficiently carbapenem-resistance determinants like the blaNDM-1 gene, all over the world. With this work we contribute with a collection set of 31 newly sequenced nosocomial A. haemolyticus isolates. Genome analysis of these sequences and others collected from RefSeq indicates that their chromosomes are organized in 12 syntenic blocks that contain most of the core genome genes. These blocks are separated by hypervariable regions that are rich in unique gene families, but also have signals of horizontal gene transfer. Genes involved in virulence or encoding different secretion systems are located inside syntenic regions and have recombination signals. The relative order of the synthetic blocks along the A. haemolyticus chromosome can change, indicating that they have been subject to several kinds of inversions. Genomes of this microorganism show large differences in gene content even if they are in the same clade. Here we also show that A. haemolyticus has an open pan-genome.

Effect of indoor environmental exposure on seminal microbiota and its application in body fluid identification

Semen is a common body fluid type in forensic sexual assault cases. It is of great significance to effectively identify semen for restoring the crime scene and determining the nature of the case. Nowadays, microbiome-based method shows as a promising tool for forensic body fluid identification. To explore the environmental impact on microbial community of semen and its traceability, 16S rDNA high-throughput sequencing was conducted to ten paired semen samples. Affected by exposure, the diversity of microbial community decreased generally as the genus Staphylococcus exhibited a relatively significant increase. However, the genus Staphylococcus, Corynebacterium, Corynebacterium_1 were observed in almost all 20 samples. Community barplot analysis and heatmap analysis showed composition of the predominant microbe in semen at the phyla and genus level maintained basically, so that it could distinguish from vaginal fluid and saliva regardless of environmental exposure. Based on these results, we believe the application of single microbial marker may limit in semen identification, but the method depending on microbial community might be useful for distinguishing semen even under indoor exposure.

Diagnosing bioremediation of crude oil-contaminated soil and related geochemical processes at the field scale through microbial community and functional genes

Purpose

Bioremediation is widely considered the most desirable procedure for remediation of oil-contaminated soil. Few studies have focused on the relationships among microbial community, functional genes of biodegradation, and geochemical processes during field bioremediation, which provide crucial information for bioremediation.

Methods

In the current study, the microbial community and functional genes related to hydrocarbon and nitrogen metabolism, combined with the soil physico-chemical properties, were used to diagnose a set of bioremediation experiments, including bioaugmentation, biostimulation, and phytoremediation, at the field scale.

Result

The results showed that the added nutrients stimulated a variety of microorganisms, including hydrocarbon degradation bacteria and nitrogen metabolism microorganisms. The functional genes reflected the possibility of aerobic denitrification in the field, which may be helpful in biodegradation. Biostimulation was found to be the most suitable of the studied bioremediation methods in the field.

Conclusion

We offer a feasible approach to obtain useful bioremediation information and assist with the development of appropriate remediation procedures. The findings improve our knowledge of the interactions between microorganisms and edaphic parameters.

Seasonal Shift in Physicochemical Factors Revealed the Ecological Variables that Modulate the Density of Acinetobacter Species in Freshwater Resources

Certain environmental variables are responsible for the survival of microorganisms in aquatic environments. The influence of these environmental factors in each season (winter, autumn, spring and summer) of the year can be used to track changes in a microbial population in freshwater resources. In this study, we assessed the effect of seasonal shifts in environmental variables including temperature, pH, total dissolved solids (TDS), total suspended solids (TSS), biochemical oxygen demand (BOD) and turbidity (TBS) among others on the density of Acinetobacter species in the Great Fish, Keiskamma and Tyhume rivers in the Eastern Cape Province, South Africa. Water samples and values of the environmental factors were taken from the rivers for 12 months. The density of presumptive Acinetobacter species was estimated from the culture of water samples on a CHROMagar selective medium, while the Acinetobacter-specific recA gene was targeted for the identification of Acinetobacter species using PCR assay. The multivariate relationship between seasons and changes in variables was created using PCA, while the effect of seasonal shifts in the environmental variables on the density of Acinetobacter species was evaluated using correlation test and topological graphs. Positive association patterns were observed between the seasons, environmental factors and the bacterial density in the rivers. In addition, temperature, TBS, TSS and BOD tended to influence the bacterial density more than other physicochemical factors in the rivers across the seasons. Of the total 1107 presumptive Acinetobacter species, 844 were confirmed as Acinetobacter species. Therefore, these findings suggested that the rivers contain Acinetobacter species that could be useful for basic and applied study in ecology or biotechnology, while their clinical relevance in causing diseases cannot be underestimated.

Cathelicidin-related Antimicrobial Peptide Contributes to Host Immune Responses Against Pulmonary Infection with Acinetobacter baumannii in Mice

Acinetobacter baumannii is known for its multidrug antibiotic resistance. New approaches to treating drug-resistant bacterial infections are urgently required. Cathelicidin-related antimicrobial peptide (CRAMP) is a murine antimicrobial peptide that exerts diverse immune functions, including both direct bacterial cell killing and immunomodulatory effects. In this study, we sought to identify the role of CRAMP in the host immune response to multidrug-resistant Acinetobacter baumannii. Wild-type (WT) and CRAMP knockout mice were infected intranasally with the bacteria. CRAMP^−/− mice exhibited increased bacterial colony-forming units (CFUs) in bronchoalveolar lavage (BAL) fluid after A. baumannii infection compared to WT mice. The loss of CRAMP expression resulted in a significant decrease in the recruitment of immune cells, primarily neutrophils. The levels of IL-6 and CXCL1 were lower, whereas the levels of IL-10 were significantly higher in the BAL fluid of CRAMP^−/− mice compared to WT mice 1 day after infection. In an in vitro assay using thioglycollate-induced peritoneal neutrophils, the ability of bacterial phagocytosis and killing was impaired in CRAMP^−/− neutrophils compared to the WT cells. CRAMP was also essential for the production of cytokines and chemokines in response to A. baumannii in neutrophils. In addition, the A. baumannii-induced inhibitor of κB-α degradation and phosphorylation of p38 MAPK were impaired in CRAMP^−/− neutrophils, whereas ERK and JNK phosphorylation was upregulated. Our results indicate that CRAMP plays an important role in the host defense against pulmonary infection with A. baumannii by promoting the antibacterial activity of neutrophils and regulating the innate immune responses.

Transcriptional Regulation of the Outer Membrane Protein A in Acinetobacter baumannii

Acinetobacter baumannii is known for its virulence in severely ill, hospitalized patients and for exhibiting multidrug resistance. A. baumannii infection treatment poses a serious problem in clinical environments. The outer membrane protein A (OmpA) of the Acinetobacter genus is involved in bacterial virulence. Regulatory factors of OmpA in the post-transcriptional stage have been previously identified. However, the regulatory factors that act before the transcriptional stage remain unclear. We investigated the A1S_0316 gene that encodes a putative transcription factor for OmpA expression in A. baumannii. A1S_0316 was purified and examined using size-exclusion chromatography, which revealed that it forms an oligomer. The binding affinity of A1S_0316 to the OmpA promoter region was also examined. We compared the binding affinity to the OmpA promotor region between A1S_0316 and the AbH-NS protein. A1S_0316 showed higher binding affinity to the OmpA promotor region than did H-NS. We examined the regulatory effect of these proteins on OmpA expression in A. baumannii using real-time qPCR and various in vitro tools. Our results indicated that A1S_0316 acts as an anti-repressor on the promotor region of the OmpA gene by inhibiting the binding of the AbH-NS protein. This study was the first demonstration of the transcriptional regulation of OmpA expression.

Computer aided ligand based screening for identification of promising molecules against enzymes involved in peptidoglycan biosynthetic pathway from Acinetobacter baumannii

A. baumannii has been considered as Priority-I as suggested by the World Health Organization (WHO) and the most critical pathogenic microorganism for causing nosocomial infection in imunno-compromised hospital-acquired patients due to multi-drug resistance (MDR). In the current study, we utilized "Computer-aided ligand-based virtual screening approach" for identification of promising molecules against Mur family proteins based on the known inhibitor (Naphthyl Tetronic Acids ((5Z)-3-(4-chlorophenyl)-4-hydroxy-5-(1-naphthylmethylene) furan-2(5H)-one)) of MurB from E. coli. The in-house library was prepared using a similarity search of a known inhibitor (Drug Bank ID: DB07296) against several relevant chemical databases. The molecules obtained from virtual screening of Naphthyl Tetronic Acids in-house library were successively subjected to physicochemical and ADMET screening. After this, the molecules which passed all the filters, subsequently subjected into interaction analysis with the drug target proteins (MurB, MurD, MurE and MurG) of A. baumanni and the results explained that four molecules were promising (CHEMBL468144, DB07296, Enamine_T5956969 and 54723243) for further molecular dynamics simulations. The free and ligand bounded proteins that undergone MD simulation are listed as follows: MurB, MurB-CHEMBL468144, MurB-DB07296, MurE, MurE-54723243, MurE-DB07296, MurD, MurD-Enamine_T5956969, MurD-DB07296, MurG, MurG-CHEMBL468144, and MurG-DB07296. Based on global and essential dynamics analysis, the stability order of molecules towards MurB (CHEMBL468144 > DB07296); MurD (Enamine_T5956969 > DB07296); MurE (54723243 > DB07296) and MurG (CHEMBL468144 > DB07296) indicates that the newly identified molecules are more promising one in comparison with the existing inhibitor. Based on all the docking and MD simulation results, the stability order of the free and ligand bounded protein are as follows; MurB and MurB-ligand complexes > MurD and MurD-ligand complexes > MurG and MurG-ligand complexes > MurE and MurE-ligand complexes. Finally, the selected compounds would be recommended for further experimental investigations and used as promising inhibitors of the infection caused by A. baumannii.

Molecular typing of multi-drug resistant Acinetobacter baumannii isolates from clinical and environmental specimens in three Iranian hospitals by pulsed field gel electrophoresis

BACKGROUND

Multi-drug resistant (MDR) Acinetobacter baumannii is one of the most important causes of nosocomial infections. The purpose of this study was to identify antibiotic resistance patterns, biofilm formation and the clonal relationship of clinical and environmental isolates of A. baumannii by Pulsed Field Gel Electrophoresis method. Forty-three clinical and 26 environmental isolates of the MDR A. baumannii were collected and recognized via API 20NE. Antibiotic resistance of the isolates was assessed by the disk diffusion method, and the biofilm formation test was done by the microtiter plate method. Pulsed Field Gel Electrophoresis (PFGE) was used to assess the genomic features of the bacterial isolates.

RESULTS

The resistance rate of clinical and environmental isolates against antibiotics were from 95 to 100%. The difference in antibiotic resistance rates between clinical and environmental isolates was not statistically significant (p > 0.05). Biofilm production capabilities revealed that 31 (44.9%), and 30 (43.5%) isolates had strong and moderate biofilm producer activity, respectively. PFGE typing exhibited eight different clusters (A, B, C, D, E, F, G, and H) with two significant clusters included A and G with 21 (30.4%) and 16 (23.2%) members respectively, which comprises up to 53.6% of all isolates. There was no relationship between biofilm formation and antibiotic resistance patterns with PFGE pulsotypes.

CONCLUSIONS

The results show that there is a close relationship between environmental and clinical isolates of A. baumannii. Cross-contamination is also very important that occurs through daily clinical activities between environmental and clinical isolates. Therefore, in order to reduce the clonal contamination of MDR A. baumannii environmental and clinical isolates, it is necessary to use strict infection control strategies.

Acinetobacter junii as a rare pathogen of urinary tract infection

Acinetobacter junii is one of more than 50 different species belonging to the genus Acinetobacter. This bacterium is rarely reported to cause human infections. Here we described a rare case of Acinetobacter junii, which grew in urine culture approximately one month after the patient was discharged from the hospital with antibiotics for a urinary tract infection, which caused left obstructing renal calculi requiring nephrostomy tube placement.

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Acinetobacter is often considered to be ubiquitous in nature.

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Acinetobacter junii is rarely reported to cause human infections.

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A rare case of Acinetobacter junii, which grew in urine culture, was described.

Detection of Antimicrobial Resistance Genes Associated with Carbapenem Resistance from the Whole-Genome Sequence of Acinetobacter baumannii Isolates from Malaysia

Background

The spread of carbapenem-resistant A. baumannii (CrAb) is gaining worldwide attention. The spread of this pathogen is largely due to its ability to acquire various resistance genes of intrinsic and extrinsic origins that confer unpredictable susceptibility to β-lactams. The aim of this study was to analyze β-lactamase genetic compositions of CrAb in Malaysia.

Methods

Whole-genome sequencing (WGS) was carried out on 13 CrAb isolates from clinical samples in Malaysia from 2011 to 2016.

Results

Endotracheal aspirate was the dominant clinical sample source (n = 6), and only one isolate was obtained from wound swab. A total of 6 sequence types (STs) of the Oxford scheme were identified, including 4 reported STs and 2 novel STs. Eleven isolates were classified into clonal complex 92 (CC92/ICII), among which ST195 and ST208 were the most prevalent STs. All 13 CrAb isolates harbored multiple β-lactamase genes. bla_OXA-23 (n = 13) and bla_OXA-66 (n = 11) were the dominant carbapenemase gene families found in these isolates. All isolates harbor bla_ADC, bla_OXA-51-like, and bla_OXA-23-like genes. bla_TEM (n = 7), bla_NDM-1 (n = 3), bla_CARB-8 (n = 1), and bla_PER-3 (n = 1) are amongst other β-lactamase genes found in this study. ISAba1 was found upstream to bla_OXA-23 (n = 13), bla_OXA-66 (n = 1), and bla_ADC (n = 11). All bla_NDM-1 isolates had ISAba125 (mobile genetic element) upstream to the genes. All isolates were positive for Tn2006/2008 and Tn2009 but were negative for Tn2007.

Conclusion

Most of the isolates were grouped under the CC92 clonal complex which belongs to international clonal lineage 2. These findings predict that carriage of carbapenem-resistant genes possibly constitutes the underlying basis of high level of international clone II prevalence. Therefore, molecular surveillance and antimicrobial stewardship are essential in implementing policies to prevent and control the spread of CrAb in hospital settings.

High-throughput sequencing approach to characterize dynamic changes of the fungal and bacterial communities during the production of sufu, a traditional Chinese fermented soybean food

Red sufu is a traditional food produced by the fermentation of soybean. In this study, sufu samples were periodically collected during the whole fermentation to investigate the dynamic changes of fungal and bacterial communities using high-throughput sequencing technology. The overall process can be divided into pre- and post-fermentation. During post-fermentation, the pH value showed a gradual decrease over time while the amino nitrogen content increased. Trichosporon, Actinomucor and Cryptococcus were the main genera in pre-fermentation while Monascus and Aspergillus were dominant in post-fermentation. This huge shift in fungal composition was caused by process procedure of pouring dressing mixture. However, the bacterial composition was not greatly changed after pouring dressing mixture, the Acinetobacter and Enterobacter were the predominant genera throughout the whole process. Furthermore, Bacillus species were first detected after adding dressing mixture, but declined abruptly to a very low level (0.07%) by the end of the fermentation. Our work demonstrates the dynamic changes of physicochemical properties and microbial composition in every fermentation stage, the knowledge of which could potentially serve as a foundation for improving the safety and quality of sufu in the future.

Evolution and distribution of resistance genes and bacterial community in water and biofilm of a simulated fish-duck integrated pond with stress

Integrated fish-duck pond is a common circular farming model in South China, besides, it is also hot-spot for the co-selection of antibiotic resistance genes (ARGs). The aim of this study was to investigate the effects of duck manure, As and cefotaxime on the bacterial community, and the evolution and distribution of ARGs and metal(loid) resistance genes (MRGs) in water and biofilm. Five groups of fish tanks included a control and four test groups. The experimental period lasted for 100 days. Six ARGs (CIT, DHA, EBC, FOX, MOX, TEM), two MRGs (arsB, arsC), and two integron genes (intI1, intI2) were tracked and detected in water and biofilm. The results showed that duck manure brought ARGs and MRGs into fish tanks. Stress factors (cefotaxime, As) increased the relative abundance of resistance genes, and this was positively correlated with stress concentrations. The biofilm was visible significantly at the end of stage 3, and the total relative abundance of resistance genes in biofilm was higher than water from stage 5 onwards. Evolution of AmpC β-lactamase resistance genes was more obvious than MRGs, especially for MOX, which increased by 3 orders of magnitude. The abundance of Flavobacterium was higher in biofilm than in water. Moreover, correlation analysis showed that both arsB and MOX were significantly correlated with intI1 (p < 0.05), which suggested a potentially dissemination risk of resistance genes. This study provides a reference for health risk assessment in integrated aquaculture environment contaminated with duck manure, antibiotics and metalloids.

Comparative genomics analysis of Acinetobacter haemolyticus isolates from sputum samples of respiratory patients

Acinetobacter haemolyticus (A. haemolyticus) is a significant Acinetobacter pathogen, and the resistance of A. haemolyticus continues to rise due to abuse of antibiotics and the frequent gene exchange between bacteria in hospital. In this study, we performed complete genome sequencing of two A. haemolyticus strains TJR01 and TJS01 to improve our understanding of pathogenic and resistance of A. haemolyticus. Both TJR01 and TJS01 contain one chromosome and two plasmids. Compared to TJS01, more virulence factors (VFs) associated pathogenicity and resistant genes were predicted in TJR01 due to T4SS and integron associated with combination and transport. Antimicrobial susceptibility results were consistent with sequencing. We suppose TJS01 was a susceptive strain and TJR01 was an acquired multidrug resistance strain due to plasmid-mediated horizontal gene transfer. We hope these findings may be helpful for clinical treatment of A. haemolyticus infection and reduce the risk of potential outbreak infection.

Detection of adeABC efllux pump encoding genes and antimicrobial effect of Mentha longifolia and Menthol on MICs of imipenem and ciprofloxacin in clinical isolates of Acinetobacter baumannii

Background

Acinetobacter baumannii is an opportunistic pathogen that causes nosocomial infections especially in patients in intensive care units (ICUs). Accordingly, the aim of our study was to detection of adeABC efllux pump encoding genes and antimicrobial effect of the essential oil of Mentha longifolia and Menthol on the minimum inhibitory concentration (MIC) of imipenem and ciprofloxacin in clinical isolates of A. baumannii.

Methods

A total of 75 clinical isolates of A. baumannii were collected. The presence of efflux pump genes was detected by polymerase chain reaction (PCR). The minimum inhibitory concentration (MIC) of the essential oil of Mentha longifolia and Menthol and their combined effect with antibiotics were measured by microbroth dilution method and fractional inhibitory concentration (FIC) index.

Results

The frequency of adeA, adeB, and adeC genes in clinical isolates of A. baumannii were 86.7, 90.7, and 92%, respectively. When the essential oil of Mentha longifolia was combined with ciprofloxacin and imipenem, MICs decreased 4- and 8-fold, respectively. In the combination of menthol with imipenem, the resistance to imipenem was reduced from 0- to 16-fold in 90% (63/70) of the isolates.

Conclusion

The presence of efflux pump genes in more than 90% of A. baumannii isolates indicates its potential role in inducing imipenem- and ciprofloxacin-resistance in this bacterium. Menthol has an antimicrobial effect as an active ingredient in Mentha longifolia. In the future, the combination of medicinal plants with antibiotics can be used as a complement in treating diseases caused by drug-resistant bacteria such as A. baumannii infections.

Insect pollination: an ecological process involved in the assembly of the seed microbiota

The assembly of the seed microbiota involves some early microbial seed colonizers that are transmitted from the maternal plant through the vascular system, while other microbes enter through the stigma. Thus, the seed microbiota consists of microbes not only recruited from the plant vascular tissues, but also from the flower. Flowers are known to be a hub for microbial transmission between plants and insects. This floral-insect exchange opens the possibility for insect-transmitted bacteria to colonize the ovule and, subsequently, the seed to pass then into the next plant generation. In this study, we evaluated the contribution of insect pollination to the seed microbiota through high-throughput sequencing. Oilseed rape (OSR) flowers were exposed to visits and pollination by honey bees (Apis mellifera), red mason bees (Osmia bicornis), hand pollinated or left for autonomous self-pollination (ASP). Sequence analyses revealed that honey bee visitation reduced bacterial richness and diversity in seeds, but increased the variability of seed microbial structure, and introduced bee-associated taxa. In contrast, mason bee pollination had minor effects on the seed microbiota. Our study provides the first evidence that insect pollination is an ecological process involved in the transmission of bacteria from flowers to seeds.

Pesticides Decrease Bacterial Diversity and Abundance of Irrigated Rice Fields

Bacteria play an important role in soil ecosystems and their activities are crucial in nutrient composition and recycling. Pesticides are extensively used in agriculture to control pests and improve yield. However, increased use of pesticides on agricultural lands results in soil contamination, which could have adverse effect on its bacterial communities. Here, we investigated the effect of pesticides commonly used on irrigated rice fields on bacterial abundance and diversity. Irrigated soil samples collected from unexposed, pesticide-exposed, and residual exposure areas were cultured under aerobic and anaerobic conditions. DNA was extracted and analysed by 16S rRNA sequencing. The results showed overall decrease in bacterial abundance and diversity in areas exposed to pesticides. Operational taxonomic units of the genera Enterobacter, Aeromonas, Comamonas, Stenotrophomonas, Bordetella, and Staphylococcus decreased in areas exposed to pesticides. Conversely, Domibacillus, Acinetobacter, Pseudomonas, and Bacillus increased in abundance in pesticide-exposed areas. Simpson and Shannon diversity indices and canonical correspondence analysis demonstrated a decrease in bacterial diversity and composition in areas exposed to pesticides. These results suggest bacteria genera unaffected by pesticides that could be further evaluated to identify species for bioremediation. Moreover, there is a need for alternative ways of improving agricultural productivity and to educate farmers to adopt innovative integrated pest management strategies to reduce deleterious impacts of pesticides on soil ecosystems.

IL-10 Protects Mice From the Lung Infection of Acinetobacter baumannii and Contributes to Bacterial Clearance by Regulating STAT3-Mediated MARCO Expression in Macrophages

Interleukin-10 plays important, yet contrasting, roles in host protection against bacterial infections and in the septic response. To determine the role of IL-10 in the host defense against Acinetobacter baumannii infection, wild-type (WT) and IL-10-deficient mice were infected intranasally with the bacteria. IL-10-deficient mice exhibited increased mortality, severe pathology, and excess production of proinflammatory cytokines and chemokines in the lungs, and increased bacterial burdens in bronchoalveolar lavage (BAL) fluids and lung homogenates after A. baumannii infection, compared to WT mice. Intranasal administration of recombinant IL-10 rescued mice from the lethality of the bacterial infection by promoting bacterial clearance and reducing production of cytokines and chemokines in the lungs. In vitro experiments revealed that IL-10 enhanced phagocytosis and bacterial killing by macrophages by upregulating the macrophage receptor with collagenous structure (MARCO). In addition, A. baumannii-induced activation of STAT3 was impaired in IL-10-deficient macrophages, which was essential for expression of MARCO. Intranasal adoptive transfer of WT macrophages resulted in significant increases in mice survival and bacterial clearance in IL-10-deficient mice infected with A. baumannii. Our results show that IL-10 played an important role in the host defense against pulmonary infection of A. baumannii by promoting the antibacterial function of macrophages by regulating MARCO expression through the STAT3-mediated pathway.

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.

High-quality treated wastewater causes remarkable changes in natural microbial communities and intI1 gene abundance

We carry out a mesocosms experiment to assess the impact of high-quality treated wastewater intended for agricultural reuse (HQWR) on freshwater bacteria seldom exposed to anthropogenic pollution. Effects were assessed by comparing the abundance and composition of bacterial communities as well as their resistance profile under control (source water from an unpolluted lake) and treatment conditions (source water mixed 1:1 with HQWR, with and without 5 μg L^-1 of cefotaxime). We investigated the effect of the different conditions on the abundance of genes encoding resistance to β-lactams and carbapenems (bla_TEM, bla_CTX-M, bla_OXA, and bla_KPC), fluoroquinolones (qnrS), tetracyclines (tetA), sulfonamides (sul2), macrolides (ermB), arsenic and cadmium (arsB and czcA, respectively), and on the gene encoding the Class 1 integron integrase (intI1). Bacterial communities exposed to HQWR showed a significant higher abundance of tetA, arsB, czcA, and intI1 genes, whereas those exposed to Cefotaxime-amended HQWR did not. Genes conferring resistance to carbapenems, β-lactams, fluoroquinolones, and macrolides were below detection limit in all treatments. Besides, the higher availability of nutrients under treatment conditions favored bacterial growth in comparison to those exposed to control conditions. Particularly, Acinetobacter spp. and Pseudomonas spp. were significantly enriched after 22 days of treatment exposure. The presence of cefotaxime (a third generation cephalosporine) in the feeding medium caused an enrichment of bacterial communities in sequences affiliated to Acinetobacter thus suggesting that these resistant forms may possess resistance genes other than those studied here (bla_CTX-M, bla_OXA, and bla_KPC). Although derived from a mesocosm experiment in continuous cultures, our results call attention to the need of refined regulations regarding the use of reclaimed water in agriculture since even high-quality treated wastewater may lead to undesired effects on receiving bacterial communities in terms of composition and dissemination of antibiotic resistance genes.

Acinetobacter pullicarnis sp. nov. isolated from chicken meat

A novel bacterial strain, named S23^T, was isolated from chicken meat of local market in Korea. Cells were Gram-negative, milky-yellow colored, non-motile and coccobacillus. The strain was obligate aerobic and catalase-positive, oxidase-negative, optimum growth temperature and pH were 25 °C and pH 7.0, respectively. On the basis of 16S rRNA gene sequence analysis, strain S23^T belongs to the genus Acinetobacter and is most closely related to Acinetobacter defluvii KCTC 52503 ^T (97.40%). The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) value between strain S23^T and its closet phylogenetic neighbors was below 76% and 17%, respectively. The G + C content of genomic DNA of strain S23^T was 41.53 mol%. The major respiratory quinone was Q-9. The major cellular fatty acids were summed feature 3 (comprising C_16:1ω7c and/or C_16:1ω6c), C_18:1ω9c, and C_16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanol-amine, and phosphatidylserine. The ANI and dDDH results and results of the genotypic analysis in combination with chemotaxonomic and physiological data demonstrated that strain S23^T represented a novel species within the genus Acinetobacter, for which the name Acinetobacter pullicarnis sp. nov. is proposed. The strain type is S23^T (= KACC 19921 ^T = JCM 33150 ^T).

The stringent response of marine bacteria - assessment of (p)ppGpp accumulation upon stress conditions

Microorganisms are particularly adapted to alterations in their environment. One of the global regulatory mechanisms involved in these adaptations is the stringent response. The unusual nucleotides, guanosine penta and tetraphosphates, (p)ppGpp act as alarmones of this response, heralding nutrient limitation and stressors. Marine bacteria encounter numerous stresses of sparse nutrient supplies and changes in physicochemical conditions. The aim of this work was to assess whether the stress conditions common in marine environment can induce the stringent response and what is a kinetic of this process. The representative bacterial species, Shewanella baltica, Acinetobacter johnsonii, Vibrio harveyi, and Escherichia coli were subjected to a variety of stressors. We analyzed the kinetics of (p)ppGpp synthesis by labeling in vivo nucleotides and analysis by thin layer chromatography. The (p)ppGpp accumulation followed the elevated temperature and amino acid starvation for all bacteria tested. The carbon and nitrogen limitation resulted in the response limited to V. harveyi and S. baltica. The DNA damaging agents induced the (p)ppGpp production in all strains, while osmotic stress did not result in significant alarmone synthesis. The representative marine bacteria species were shown to induce with varying extent the stringent response upon the onset of stress and limitation conditions. Importantly, the in vivo labeling and subsequent separation of the nucleotides by thin layer chromatography serves as a valid method for the analysis of the stringent response and (p)ppGpp accumulation in environmental bacteria.

Subsurface Microbial Ecology at Sediment-Groundwater Interface in Sulfate-Rich Playa; White Sands National Monument, New Mexico

The hypersaline sediment and groundwater of playa lake, Lake Lucero, at the White Sands National Monument in New Mexico were examined for microbial community composition, geochemical gradients, and mineralogy during the dry season along a meter and a half depth profile of the sediment vs. the groundwater interface. Lake Lucero is a highly dynamic environment, strongly characterized by the capillary action of the groundwater, the extreme seasonality of the climate, and the hypersalinity. Sediments are predominantly composed of gypsum with minor quartz, thenardite, halite, quartz, epsomite, celestine, and clays. Geochemical analysis has revealed the predominance of nitrates over ammonium in all of the analyzed samples, indicating oxygenated conditions throughout the sediment column and in groundwater. Conversely, the microbial communities are primarily aerobic, gram-negative, and are largely characterized by their survival adaptations. Halophiles and oligotrophs are ubiquitous for all the samples. The very diverse communities contain methanogens, phototrophs, heterotrophs, saprophytes, ammonia-oxidizers, sulfur-oxidizers, sulfate-reducers, iron-reducers, and nitrifiers. The microbial diversity varied significantly between groundwater and sediment samples as their temperature adaptation inferences that revealed potential psychrophiles inhabiting the groundwater and thermophiles and mesophiles being present in the sediment. The dynamism of this environment manifests in the relatively even character of the sediment hosted microbial communities, where significant taxonomic distinctions were observed. Therefore, sediment and groundwater substrates are considered as separate ecological entities. We hope that the variety of the discussed playa environments and the microorganisms may be considered a useful terrestrial analog providing valuable information to aid future astrobiological explorations.

Dynamics of microbial contaminants is driven by selection during ethanol production

Brazil is the second largest ethanol producer in the world and largest using sugarcane feedstock. Bacteria contamination is one of the most important issues faced by ethanol producers that seek to increase production efficiency. Each step of production is a selection event due to the environmental and biological changes that occur. Therefore, we evaluated the influence of the selection arising from the ethanol production process on diversity and composition of bacteria. Our objectives were to test two hypotheses, (1) that species richness will decrease during the production process and (2) that lactic acid bacteria will become dominant with the advance of ethanol production. Bacterial community assemblage was accessed using 16S rRNA gene sequencing from 19 sequential samples. Temperature is of great importance in shaping microbial communities. Species richness increased between the decanter and must steps of the process. Low Simpson index values were recorded at the fermentation step, indicating a high dominance of Lactobacillus. Interactions between Lactobacillus and yeast may be impairing the efficiency of industrial ethanol production.

Dietary daidzein improved intestinal health of juvenile turbot in terms of intestinal mucosal barrier function and intestinal microbiota

A 12-week feeding trial was conducted to investigate the effect of dietary daidzein on the intestinal mucosal barrier function and the intestinal microbiota profile of juvenile turbot (Scophthalmus maximus L.). Three isonitrogenous and isolipidic experimental diets were formulated to contain 0 (FM), 40 (D.40) and 400 (D.400) mg kg^-1 daidzein, respectively. Fish fed D.400 had significantly lower growth performance than fish fed D.40. Dietary daidzein significantly increased the feed efficiency, while significantly decreased the feed intake. Daidzein supplementation increased the activity of total anti-oxidative capacity and the gene expression of anti-inflammatory cytokine transforming growth factor-β1, Mucin-2 and tight junction proteins (Tricellulin, Zonula occludens-1 transcript variant 1, Zonula occludens-1 transcript variant 2 and Claudin-like and Occludin), and down-regulated the gene expression of pro-inflammatory cytokines interleukin-1β and tumor necrosis factor-α in the intestine of turbot. Dietary daidzein increased intestinal microbial diversities, the abundance of several short chain fatty acids producers, and decreased the abundance of some potential pathogenic bacteria. However, D.400 had dual effects on lactic acid bacteria and increased the abundance of potential harmful bacterium Prevotella copri. Collectively, dietary daidzein at the levels of 40 and 400 mg kg^-1 could enhance the intestinal mucosal barrier function and alter the intestinal microbiota of turbot. However, high dose of daidzein must be treated with caution for its unclear effects on intestinal microbiota of turbot in the present study.

Impacts of environmental complexity on respiratory and gut microbiome community structure and diversity in growing pigs

The limited understanding of the interaction between rearing environment of the growing pig and the pig’s microbial community impedes efforts to identify the optimal housing system to maximize animal health and production. Accordingly, we characterized the impact of housing complexity on shaping the respiratory and gut microbiota of growing pig. A total of 175 weaned pigs from 25 litters were randomly assigned within liter to either simple slatted-floor (S) or complex straw-based rearing ecosystem (C). Beside the floor swabs samples, fecal swabs and mucosal scraping samples from bronchus, ileum, and colon were collected approximately 164 days post-weaning at the time of slaughter. The S ecosystem seems to increase the α-diversity of respiratory and gut microbiota. Moreover, the C-raised pigs showed 35.4, 89.2, and 60.0% reduction in the Firmicutes/Bacteroidetes ratio than the S-raised pigs at bronchus, ileum, and colon, respectively. The unfavorable taxa Psychrobacter, Corynebacterium, Actinobacteria, and Neisseria were the signature taxa of C environment-associated microbial community. Therefore, the microbiota of S-raised pigs seems to show higher density of the most essential and beneficial taxa than the C-raised pigs. We preliminarily conclude that increasing the physical complexity of rearing environment seems to provide suboptimal conditions for establishing a healthy microbial community in the growing pigs.

Virulence determinants and biofilm formation of Acinetobacter baumannii isolated from hospitalized patients

Introduction

Acinetobacter baumannii are nosocomial bacteria that are responsible for outbreaks and severe infections in hospitalized patients globally. The major target of this study was the characterization of virulence determinants and biofilm formation of A. baumannii isolates from hospitalized patients.

Methods

In total, 100 A. baumannii were collected from three hospitals in Tehran, Iran, 2017-2018. The isolates were assessed using phenotypic and genotypic methods and then screened for virulence factor encoding genes such as plcN and lasB using conventional polymerase chain reaction. Furthermore, bacterial biofilm formation, motility and hemolytic and proteolytic activities were assessed.

Results

Of 100 A. baumannii isolates, 20 isolates included plcN and four isolates included lasB using PCR assay. Overall, 21 isolates were negative for biofilm formation while 45, 20 and 14 of the total isolates were reported as weak, moderate and strong biofilm producers, respectively. All isolates were positive for bap genes using PCR. Moreover, 35 isolates were motile on Luria-Bertani media, 47 isolates were α-hemolytic on Brucella blood agar media and all isolates displayed proteolytic activity.

Conclusions

Healthcare-associated infections with A. baumannii are a major concern, importantly due to their potency to acquire virulence factor genes. Therefore, shedding light in the discovery of new antimicrobial and/or therapeutic agents against virulent A. baumannii strains seem to be necessary.

New Shuttle Vectors for Real-Time Gene Expression Analysis in Multidrug-Resistant Acinetobacter Species: In Vitro and In Vivo Responses to Environmental Stressors

The Acinetobacter genus includes species of opportunistic pathogens and harmless saprophytes. The type species, Acinetobacter baumannii, is a nosocomial pathogen renowned for being multidrug resistant (MDR). Despite the clinical relevance of infections caused by MDR A. baumannii and a few other Acinetobacter spp., the regulation of their pathogenicity remains elusive due to the scarcity of adequate genetic tools, including vectors for gene expression analysis. Here, we report the generation and testing of a series of Escherichia coli-Acinetobacter promoter-probe vectors suitable for gene expression analysis in Acinetobacter spp. These vectors, named pLPV1Z, pLPV2Z, and pLPV3Z, carry both gentamicin and zeocin resistance markers and contain lux, lacZ, and green fluorescent protein (GFP) reporter systems downstream of an extended polylinker, respectively. The presence of a toxin-antitoxin gene system and the high copy number allow pLPV plasmids to be stably maintained even without antibiotic selection. The pLPV plasmids can easily be introduced by electroporation into MDR A. baumannii belonging to the major international lineages as well as into species of the Acinetobacter calcoaceticus-A. baumannii complex. The pLPV vectors have successfully been employed to study the regulation of stress-responsive A. baumannii promoters, including the DNA damage-inducible uvrABC promoter, the ethanol-inducible adhP and yahK promoters, and the iron-repressible promoter of the acinetobactin siderophore biosynthesis gene basA A lux-tagged A. baumannii ATCC 19606^T strain, carrying the iron-responsive pLPV1Z::PbasA promoter fusion, allowed in vivo and ex vivo monitoring of the bacterial burden in the Galleria mellonella infection model.IMPORTANCE The short-term adaptive response to environmental cues greatly contributes to the ecological success of bacteria, and profound alterations in bacterial gene expression occur in response to physical, chemical, and nutritional stresses. Bacteria belonging to the Acinetobacter genus are ubiquitous inhabitants of soil and water though some species, such as Acinetobacter baumannii, are pathogenic and cause serious concern due to antibiotic resistance. Understanding A. baumannii pathobiology requires adequate genetic tools for gene expression analysis, and to this end we developed user-friendly shuttle vectors to probe the transcriptional responses to different environmental stresses. Vectors were constructed to overcome the problem of antibiotic selection in multidrug-resistant strains and were equipped with suitable reporter systems to facilitate signal detection. By means of these vectors, the transcriptional response of A. baumannii to DNA damage, ethanol exposure, and iron starvation was investigated both in vitro and in vivo, providing insights into A. baumannii adaptation during stress and infection.

Antimicrobial Activity of Selected Antimicrobial Peptides Against Planktonic Culture and Biofilm of Acinetobacter baumannii

Acinetobacter baumannii is one of the most challenging pathogens, on account of its predisposition to develop resistance leading to severe, difficult-to-treat infections. As these bacteria are more usually isolated from nosocomial infections, the new therapeutic options are demanded. Antimicrobial peptides (AMPs) are compounds likely to find application in the treatment of A. baumannii. These compounds exhibit a wide spectrum of antimicrobial activity and were found to be effective against biofilm. In this study, eight AMPs, namely aurein 1.2, CAMEL, citropin 1.1., LL-37, omiganan, r-omiganan, pexiganan, and temporin A, were tested for their antimicrobial activity. A reference strain of A. baumannii ATCC 19606 was used. Antimicrobial assays included determination of the minimum inhibitory concentration and the minimum biofilm eradication concentration. Considering the fact that the majority of A. baumannii infections are associated with mechanical ventilation and the use of indwelling devices, the activity against biofilm was assessed on both a polystyrene surface and tracheal tube fragments. In addition, cytotoxicity (HaCaT) was determined and in vitro selectivity index was calculated.

A hydrocarbon-contaminated aquifer reveals a Piggyback-the-Persistent viral strategy

Subsurface environments hold the largest reservoir of microbes in the biosphere. They play essential roles in transforming nutrients, degrading contaminants and recycling organic matter. Here, we propose a previously unrecognised fundamental microbial process that influences aquifer bioremediation dynamics and that applies to all microbial communities. In contrast to previous models, our proposed Piggyback-the-Persistent (PtP) mechanism occurs when viruses become more dominated by those exhibiting temperate rather than lytic lifestyles driven by persistent chemicals (in our case chlorinated-hydrocarbon pollutants) that provide long-term carbon sources and that refocus the aquifer carbon cycle, thus altering the microbial community. In this ultra-oligotrophic system, the virus:microbial ratio (VMR) ranges from below the detection limit of 0.0001 to 0.6, well below the common aquatic range of 3-10. Shortest-average-path network analysis revealed VMR and trichlorethene (TCE) as nodes through which ecosystem information and biomass most efficiently pass. Novel network rearrangement revealed a hierarchy of Kill-the-Winner (KtW), Piggyback-the-Winner (PtW) and PtP nodes. We propose that KtW, PtW and PtP occur simultaneously as competing strategies, with their relative importance depending on conditions at a particular time and location with unusual nutrient sources, such as TCE, appearing to contribute to a shift in this balance between viral mechanisms.

Physiological and transcriptional comparison of acetate catabolism between Acinetobacter schindleri ACE and Escherichia coli JM101

Acinetobacter bacteria preferentially use gluconeogenic substrates instead of hexoses or pentoses. Accordingly, Acinetobacter schindleri ACE reaches a high growth rate on acetate but is unable to grow on glucose, xylose or arabinose. In this work, we compared the physiology of A. schindleri ACE and Escherichia coli JM101 growing on acetate as the carbon source. In contrast to JM101, ACE grew on acetate threefold faster, had a twofold higher biomass yield, and a 45% higher specific acetate consumption rate. Transcriptional analysis revealed that genes like ackA, pta, aceA, glcB, fumA, tktA and talA were overexpressed while acsA, sfcA, ppc and rpiA were underexpressed in ACE relative to JM101. This transcriptional profile together with carbon flux balance analysis indicated that ACE forms acetyl-CoA preferentially by the AckA-Pta (acetate kinase-phosphotransacetylase) pathway instead of Acs (acetyl-CoA synthetase) and that the glyoxylate shunt and tricarboxylic acid cycle are more active in ACE than in JM101. Moreover, in ACE, ribose 5-phosphate and erythrose 4-phosphate are formed from trioses, and NADPH is mainly produced by isocitrate dehydrogenase. This knowledge will contribute to an understanding of the carbon metabolism of Acinetobacter species of medical, biotechnological and microbiological relevance.

A comparative study of microbial community and dynamics of Asaia in the brown planthopper from susceptible and resistant rice varieties

BACKGROUND

The brown planthopper (BPH) is likely the most destructive, piercing and sucking monophagous insect pest of rice that causes substantial economic losses to farmers. Although yeast-like symbionts (YLS) and virus transmission have been observed in the BPH, the bacterial population inhabiting the BPH has received minimal research attention. Labelling BPH-associated bacterial species may shed light on BPH biology and the interaction between the BPH and rice to provide novel approaches for the efficient control of this insect pest.

RESULTS

We examined RNA-seq results to identify bacterial populations present in different generations of BPHs maintained on susceptible or resistant rice varieties. Overall, 87 operational taxonomic units (OTUs) were determined from the BPH-F0, F6 and F16 generations. These OTUs had Shannon and Simpson index values of 0.37-0.6 and 0.56-1.19, respectively. The evenness values of 0.7-1.00 showed the vastness of the bacterial diversity recovered from the BPH samples. The results showed high species diversity in the BPHs collected from susceptible rice and a high number of members of unclassified bacteria in the BPHs isolated from resistant rice. We noticed that Proteobacteria OTUs were predominant across all samples. Furthermore, PCR data of Asaia species showed variable DNA amplification across the BPH samples collected from susceptible or resistant varieties. The identification of Asaia in BPH eggs and BPH-egg-infected rice revealed its influence on the interaction between the BPH egg and rice.

CONCLUSIONS

The BPHs had clear differences in their microbiomes and in their ability to feed on different rice hosts. These variations could have an essential impact on host adaptation and interaction. These results provide a better understanding of the bacterial diversity and interaction of the microbiome of different generations of BPHs. Furthermore, PCR data of Asaia sp. variation across the BPH samples (isolated from different host genotypes selected from the field and laboratory, including BPH eggs and egg-infected rice tissues), suggest that Asaia could be an important member of the insect microbiome involved in adaptation, its interaction with rice and, most importantly, as a paratransgenic tool for insect control.

Dissimilatory iron and sulfate reduction by native microbial communities using lactate and citrate as carbon sources and electron donors

The bacterial (dissimilatory) iron and sulfate reduction (BIR and BSR) are intimately linked to the biogeochemical cycling of C, Fe, and S in acid mine drainage (AMD) environments. This study examined the response of native microbial communities to the reduction of iron and sulfate in bench experimental systems. Results showed that the reduction of ferric iron and sulfate took place when the electron acceptors coexist. Existence of Fe(III) can postpone the reduction of sulfate, but can enhance the reduction rate. Cultures grown in the presence of 10 mM iron can reach the final level of sulfate bio-reduction rate (~100%) after 35 days incubation. 16 S rDNA -based microbial community analysis revealed that the three genera Anaeromusa, Acinetobacter and Bacteroides were dominated in the ferric-reducing conditions. SRB (Desulfobulbus, Desulfosporosinus and Desulfovibrio) were dominated in the sulfate reduction process. Results in this study highlighted the highly coupled nature of C, Fe, and S biogeochemical cycles in AMD and provided insights into the potential of environmental remediation by native microbial.

Floc-size effects of the pathogenic bacteria in a membrane bioreactor plant

The size nature of sludge flocs could affect the occurrence and distribution of bacterial pathogens in wastewater treatment plants (WWTPs). In this study, the floc-size dependence of bacterial pathogens in the activated sludge of a WWTP was investigated using high-throughput metagenomic sequencing approaches. The results showed that a total of 423 pathogenic species belonging to 123 genera were identified in the three size-fractionated flocs. Also, we found that all the pathogens on the WHO's global priority pathogens list were detected in the size-fractionated flocs, with relative abundance of 0.4%, 0.3% and 0.3% for large-size, medium-size and small-size flocs, respectively, indicating the severe human and environmental health risks of activated sludge. Importantly, our results revealed that the pathogenic species showed a clear floc-size dependent distribution manner, leading to significant differences (P < 0.05) of pathogenic communities among the size-fractionated flocs. Additionally, by partitioning pathogens based on the occurrence and significant difference in abundances, we suggested the following distribution features: 1) large flocs-associated pathogens, such as Borrelia recurrentis, Actinobacillus ureae and Campylobacter gracilis; 2) medium flocs-associated pathogens, such as Mycobacterium szulgai and Ureaplasma urealyticum; and 3) small flocs-associated pathogens, such as Rickettsia akari, Staphylococcus anginosus and Helicobacter cinaedi. Overall, this study provides a comprehensive understanding of pathogens in activated sludge, which is expected to aid in assessment and management of pathogen risks.

Yeast-Bacterium Interactions: The Next Frontier in Nectar Research

Beyond its role as a reward for pollinators, floral nectar also provides a habitat for specialized and opportunistic yeasts and bacteria. These microbes modify nectar chemistry, often altering mutualistic relationships between plants and pollinators in ways that we are only beginning to understand. Many studies on this multi-partite system have focused on either yeasts or bacteria without consideration of yeast-bacterium interactions, but recent evidence suggests that such interactions drive the assembly of nectar microbial communities and its consequences for pollination. Unexplored potential mechanisms of yeast-bacterium interactions include the formation of physical complexes, nutritional interactions, antibiosis, signaling-based interactions, and horizontal gene transfer. We argue that studying these mechanisms can elucidate how nectar microbial communities are established and affect plant fitness via pollinators.

Coping with low water activities and osmotic stress in Acinetobacter baumannii: significance, current status and perspectives

Multidrug resistant (MDR) pathogens are one of the most pressing challenges of contemporary health care. Acinetobacter baumannii takes a predominant position, emphasized in 2017 by the World Health Organization. The increasing emergence of MDR strains strengthens the demand for new antimicrobials. Possible targets for such compounds might be proteins involved in resistance against low water activity environments, since A. baumannii is known for its pronounced resistance against desiccation stress. Despite the importance of desiccation resistance for persistence of this pathogen in hospitals, comparable studies and precise data on this topic are rare and the mechanisms involved are largely unknown. This review aims to give an overview of the studies performed so far and the current knowledge on genes and proteins important for desiccation survival. 'Osmotic stress' is not identical to 'desiccation stress', but the two share the response of bacteria to low water activities. Osmotic stress resistance is in general studied much better, and in recent years it turned out that accumulation of compatible solutes in A. baumannii comprises some special features such as the bifunctional enzyme MtlD synthesizing the unusual solute mannitol. Furthermore, the regulatory pathways, as understood today, will be discussed.

Ultrasound combined with dilute acid pretreatment of grass for improvement of fermentative hydrogen production

In this study, the dilute acid pretreatment combined with ultrasound was applied to improve fermentative hydrogen production from grass. The experimental results indicated that SCOD and soluble carbohydrate contents of grass was improved by 98.6% and 236.9% after the combined treatment, respectively. Surface morphology (SEM and AFM) and crystallinity analysis revealed that the combined pretreatment process could effectively destroyed the biomass structure and increased their surface area. Owing to the increased soluble organics proportion and better enzymatic accessibility of residual solids, the hydrogen yield reached 42.2 mL/g-dry grass after the combined treatment, which was 311.7%, 190.0% and 35.0% higher in comparison with the control, individual ultrasound and acid pretreated groups, respectively. Meanwhile, the combined treatment also increased the substrate utilization efficiency and induced a more efficient fermentation pathway. Bacterial community analysis revealed that more enrichment of Clostridium and less enrichment of Enterococcus contributed to the improved hydrogen production.

Seasonal Occurrence and Carbapenem Susceptibility of Bovine Acinetobacter baumannii in Germany

Acinetobacter baumannii is one of the leading causes of nosocomial infections in humans. To investigate its prevalence, distribution of sequence types (STs), and antimicrobial resistance in cattle, we sampled 422 cattle, including 280 dairy cows, 59 beef cattle, and 83 calves over a 14-month period. Metadata, such as the previous use of antimicrobial agents and feeding, were collected to identify putative determining factors. Bacterial isolates were identified via MALDI-TOF/MS and PCR, antimicrobial susceptibility was evaluated via VITEK2 and antibiotic gradient tests, resistance genes were identified by PCR. Overall, 15.6% of the cattle harbored A. baumannii, predominantly in the nose (60.3% of the A. baumannii isolates). It was more frequent in dairy cows (21.1%) than in beef cattle (6.8%) and calves (2.4%). A seasonal occurrence was shown with a peak between May and August. The rate of occurrence of A. baumannii was correlated with a history of use of 3rd generation cephalosporins in the last 6 months prior to sampling Multilocus sequence typing (Pasteur scheme) revealed 83 STs among 126 unique isolates. Nine of the bovine STs have previously been implicated in human infections. Besides known intrinsic resistance of the species, the isolates did not show additional resistance to the antimicrobial substances tested, including carbapenems. Our data suggest that cattle are not a reservoir for nosocomial A. baumannii but carry a highly diverse population of this species. Nevertheless, some STs seem to be able to colonize both cattle and humans.

Bacterial and Biodeterioration Analysis of the Waterlogged Wooden Lacquer Plates from the Nanhai No. 1 Shipwreck

To protect the lacquer plates from the Nanhai No. 1 shipwreck from being corroded by microorganisms, a series of studies were conducted on the four water-stored samples. The water samples were collected from the vessel where the lacquerware was stored in June and December 2017. In our study, high-throughput sequencing was conducted to reveal predominant bacterial communities. Then, three different media were used to isolate the dominant bacteria, and the 16S rRNA genes were sequenced. Next, we tested the degradation activity of lignin and cellulose by the isolated bacterial strains. After being cultured on a medium containing carboxylmethylcellulose (CMC), almost all the isolated strains (except Microbacterium sp. NK-NH4, Ochrobactrum sp. NK-NH9, and Bacillus megaterium NK-NH10) showed the capacity for cellulose degradation. In addition, the lignin peroxidase (Lip) and laccase activity of the strains were shown by culturing the strains on one medium with azure and on another medium with Remazol brilliant blue. The results indicated that the Lip activity of all the strains was low, whereas the laccase activity of Microbacterium sp. NK-NH4, Bacillus tequilensis NK-NH5, Bacillus subtilis NK-NH6, Bacillus megaterium NK-NH10, and Bacillus velezensis NK-NH11 was relatively high. Finally, we tested the bacteriostatic efficacy of four biocides—Preventol® D7, BIT 20N, P91, and Euxyl® K100. We found that most strains were sensitive to D7 and 20N, while K100 had almost no impact.

A culture-dependent and metagenomic approach of household drinking water from the source to point of use in a developing country

Rural households in developing countries rely on communal water supplies and household water frequently becomes contaminated following its collection, transportation and during its storage. Using culture-dependent and -independent techniques, we examined the changes in microbial water quality between communal tap water and household water storage in a rural area of Cameroon, Africa. The culturable fecal indicator bacteria (FIB) were used to assess the potential health risks associated with different household water storage conditions (e.g., type of container and open vs. closed container) and interventions (e.g., water storage days, cleaned on the last day of use, and hygiene practices). Only the amount of days the water was stored significantly differed (p-value < 0.05), which showed that potential health risks increased when water was stored for more than 3 days. The higher abundance of molecular FIB in biofilm than household water suggested that omnipresent biofilm in household water could potential health risk. The high-throughput sequencing revealed that the most abundant phylum was Proteobacteria, followed by Actinobacteria and Bacteroidetes in both the water and the biofilm samples. Bacterial genera seen in biofilm bacteria, such as Pseudomonas, Acinetobacter and Comamonas. Acinetobacter, Chryseobacterium, Stenotrophomonas and Corynebacterium, were relatively more abundant in the biofilm than in the water. Potential bacterial pathogens including Acinetobacter baumannii, Citrobacter freundii, Stenotrophomonas maltophilia and Haemophilus influenza, were detected in household water and biofilm. The microbial quality might be affected by water-storage time and households repeatedly using the same water storage containers without proper sanitization, triggering microbial regrowth and biofilm formation on water containers. Higher bacterial diversity and potentially pathogenic bacteria found in the biofilm samples of a household water supply are unhealthy for the house's inhabitants. It is important to develop interventions aimed at preventing the formation of these dangerous biofilms in a communal water supply.

Dynamic membrane bioreactor performance enhancement by powdered activated carbon addition: Evaluation of sludge morphological, aggregative and microbial properties

The effects of powdered activated carbon (PAC) addition on sludge morphological, aggregative and microbial properties in a dynamic membrane bioreactor (DMBR) were investigated to explore the enhancement mechanism of pollutants removal and filtration performance. Sludge properties were analyzed through various analytical measurements. The results showed that the improved sludge aggregation ability and the evolution of microbial communities affected sludge morphology in PAC-DMBR, as evidenced by the formation of large, regularly shaped and strengthened sludge flocs. The modifications of sludge characteristics promoted the formation process and filtration flux of the dynamic membrane (DM) layer. Additionally, PAC addition did not exert very significant influence on the propagation of eukaryotes (protists and metazoans) and microbial metabolic activity. High-throughput pyrosequencing results indicated that adding PAC improved the bacterial diversity in activated sludge, as PAC addition brought about additional microenvironment in the form of biological PAC (BPAC), which promoted the enrichment of Acinetobacter (13.9%), Comamonas (2.9%), Flavobacterium (0.31%) and Pseudomonas (0.62%), all contributing to sludge flocs formation and several (such as Acinetobacter) capable of biodegrading relatively complex organics. Therefore, PAC addition could favorably modify sludge properties from various aspects and thus enhance the DMBR performance.