Demystifying polyphosphate-accumulating organisms relevant to wastewater treatment: A review of their phylogeny, metabolism, and detection

Currently, the most cost-effective and efficient method for phosphorus (P) removal from wastewater is enhanced biological P removal (EPBR) via polyphosphate-accumulating organisms (PAOs). This study integrates a literature review with genomic analysis to uncover the phylogenetic and metabolic diversity of the relevant PAOs for wastewater treatment. The findings highlight significant differences in the metabolic capabilities of PAOs relevant to wastewater treatment. Notably, Candidatus Dechloromonas and Candidatus Accumulibacter can synthesize polyhydroxyalkanoates, possess specific enzymes for ATP production from polyphosphate, and have electrochemical transporters for acetate and C4-dicarboxylates. In contrast, Tetrasphaera, Candidatus Phosphoribacter, Knoellia, and Phycicoccus possess PolyP-glucokinase and electrochemical transporters for sugars/amino acids. Additionally, this review explores various detection methods for polyphosphate and PAOs in activated sludge wastewater treatment plants. Notably, FISH-Raman spectroscopy emerges as one of the most advanced detection techniques. Overall, this review provides critical insights into PAO research, underscoring the need for enhanced strategies in biological phosphorus removal.

Functional characterization of a TerC family protein of Riemerella anatipestifer in manganese detoxification and virulence

Manganese (Mn) is an essential element for bacteria, but the overload of manganese is toxic. In a previous study, we showed that the cation diffusion facilitator protein MetA and the resistance-nodulation-division efflux pump MetB are responsible for Mn efflux in the bacterial pathogen Riemerella anatipestifer CH-1. However, whether this bacterium encodes additional manganese efflux proteins is unclear. In this study, we show that R. anatipestifer CH-1 encodes a tellurium resistance C (TerC) family protein with low similarity to other characterized TerC family proteins. Compared to the wild type (WT), the terC mutant of R. anatipestifer CH-1 (∆terC) is sensitive to Mn(II) intoxication. The ability of TerC to export manganese is higher than that of MetB but lower than that of MetA. Consistently, terC deletion (∆terC) led to intracellular accumulation of Mn2+ under excess manganese conditions. Further study showed that ∆terC was more sensitive than the WT to the oxidant hypoclorite but not to hydrogen peroxide. Mutagenesis studies showed that the mutant at amino acid sites of Glu116 (E116), Asp122 (D122), Glu245 (E245) Asp248 (D248), and Asp254 (D254) may be involved in the ability of TerC to export manganese. The transcription of terC was upregulated under excess manganese and downregulated under iron-limited conditions. However, this was not dependent on the manganese metabolism regulator MetR. In contrast to a strain lacking the manganese efflux pump MetA or MetB, the terC mutant is attenuated in virulence in a duckling model of infection due to increased sensitivity to duck serum. Finally, comparative analysis showed that homologs of TerC are distributed across the bacterial kingdom, suggesting that TerC exerts a conserved manganese efflux function.IMPORTANCERiemerella anatipestifer is a notorious bacterial pathogen of ducks and other birds. In R. anatipestifer, the genes involved in manganese efflux have not been completely identified, although MetA and MetB have been identified as two manganese exporters. Additionally, the function of TerC family proteins in manganese efflux is controversial. Here, we demonstrated that a TerC family protein helps prevent Mn(II) intoxication in R. anatipestifer and that the ability of TerC to export manganese is intermediate compared to that of MetA and MetB. Sequence analysis and mutagenesis studies showed that the conserved key amino sites of TerC are Glu116, Asp122, Glu245, Asp248, and Asp254. The transcription of terC was regulated by manganese excess and iron limitation. Finally, we show that TerC plays a role in the virulence of R. anatipestifer due to the increased sensitivity to duck serum, rather than the increased sensitivity to manganese. Taken together, these results expand our understanding of manganese efflux and the pathogenic mechanisms of R. anatipestifer.

Complete genome sequence of Brucella pseudintermedia ASAG-D25, isolated from the wheat ear

Brucella pseudintermedia ASAG-D25 was isolated from the wheat ear sample in Xuzhou City, Jiangsu Province, China. The complete genome sequence of B. pseudintermedia will provide an important resource for better understanding of the genetic features of the species within the family of Brucellaceae.

Evaluation of Bile Salts on the Survival and Modulation of Virulence of Aliarcobacter butzleri

Aliarcobacter butzleri is a Gram-negative bacterium associated with infections of the gastrointestinal tract and widely distributed in various environments. For successful infection, A. butzleri should be able to tolerate various stresses during gastrointestinal passage, such as bile. Bile represents an antimicrobial host barrier that acts against external noxious agents and consists of a variety of bile salts. The intestinal bile salts act as detergents involved in the antimicrobial host defense; although, on the bacterial side, they could also serve as a signal to activate virulence mechanisms. The aim of this work was to understand the effects of bile salts on the survival and virulence of A. butzleri. In our study, A. butzleri was able to survive in the presence of human physiological concentrations of bile salts. Regarding the virulence features, an increase in cellular hydrophobicity, a decrease in motility and expression of flaA gene, as well as an increase in biofilm formation with a concomitant change in the type of biofilm structure were observed in the presence of sub-inhibitory concentration of bile salts. Concerning adhesion and invasion ability, no significant difference was observed. Overall, the results demonstrated that A. butzleri is able to survive in physiological concentrations of bile salts and that exposure to bile salts could change its virulence mechanisms.

Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021

Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria (Including Members of the Phylum Planctomycetota) Isolated from Aquatic Host Species Described in 2018 to 2021

Increased interest in farmed aquatic species, aquatic conservation measures, and microbial metabolic end-product utilization have translated into a need for awareness and recognition of novel microbial species and revisions to bacterial taxonomy. Because this need has largely been unmet, through a 4-year literature review, we present lists of novel and revised bacterial species (including members of the phylum Planctomycetota) derived from aquatic hosts that can serve as a baseline for future biennial summaries of taxonomic revisions in this field. Most new and revised taxa were noted within oxidase-positive and/or nonglucose fermentative Gram-negative bacilli, including members of the Tenacibaculum, Flavobacterium, and Vibrio genera. Valid and effectively published novel members of the Streptococcus, Erysipelothrix, and Photobacterium genera are additionally described from disease pathogenesis perspectives.

Update on Accepted Novel Bacterial Isolates Derived from Human Clinical Specimens and Taxonomic Revisions Published in 2020 and 2021

A number of factors, including microbiome analyses and the increased utilization of whole-genome sequencing in the clinical microbiology laboratory, has contributed to the explosion of novel prokaryotic species discovery, as well as bacterial taxonomy revision. This review attempts to summarize such changes relative to human clinical specimens that occurred in 2020 and 2021, per primary publication in the International Journal of Systematic and Evolutionary Microbiology or acceptance on Validation Lists published by the International Journal of Systematic and Evolutionary Microbiology. Of particular significance among valid and effectively published taxa within the past 2 years were novel Corynebacterium spp., coagulase-positive staphylococci, Pandoraea spp., and members of family Yersiniaceae. Noteworthy taxonomic revisions include those within the Bacillus and Lactobacillus genera, family Staphylococcaceae (including unifications of subspecies designations to species level taxa), Elizabethkingia spp., and former members of Clostridium spp. and Bacteroides spp. Revisions within the Brucella genus have the potential to cause deleterious effects unless the relevance of such changes is properly communicated by microbiologists to stakeholders in clinical practice, infection prevention, and public health.

The Prevalence of Arcobacteraceae in Aquatic Environments: A Systematic Review and Meta-Analysis

Members of the family Arcobacteraceae are distributed widely in aquatic environments, and some of its species have been associated with human and animal illness. However, information about the diversity and distribution of Arcobacteraceae in different water bodies is still limited. In order to better characterize the health risk posed by members in the family Arcobacteraceae, a systematic review and meta-analysis-based method was used to investigate the prevalence of Arcobacteraceae species in aquatic environments based on available data published worldwide. The database search was performed using related keywords and considering studies up to February 2021. The pooled prevalence in aquatic environments was 69.2%, ranging from 0.6 to 99.9%. These bacteria have a wide geographical distribution, being found in diverse aquatic environments with the highest prevalence found in raw sewage and wastewater treatment plants (WWTP), followed by seawater, surface water, ground water, processing water from food processing plants and water for human consumption. Assessing the effectiveness of treatments in WWTP in eliminating this contamination, it was found that the wastewater treatment may not be efficient in the removal of Arcobacteraceae. Among the analyzed Arcobacteraceae species, Al. butzleri was the most frequently found species. These results highlight the high prevalence and distribution of Arcobacteraceae in different aquatic environments, suggesting a risk to human health. Further, it exposes the importance of identifying and managing the sources of contamination and taking preventive actions to reduce the burden of members of the Arcobacteraceae family.

Bacterial nomenclature in the era of genomics

The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice while minimizing difficulties. Adoption of linguistic pragmatism-obeying the rules while treating recommendations as merely optional-will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.

First case of diarrhea due to Aliarcobacter butzleri (formerly Arcobacter butzleri) in Ecuador

The first case of acute watery diarrhea disease due to Aliarcobacter butzleri (formerly Arcobacter butzleri) in Ecuador is reported. An infant presented with moderate protein-calorie malnutrition, dehydration and anemia. A curved Gram-negative organism was isolated from stools, having been preliminarily identified by phenotypic characteristics. Definitive identification was achieved by multiplex PCR. Aliarcobacter butzleri was the only pathogenic microorganism isolated. No other entero-pathogens, enterovirus or parasites were found. Our findings strongly suggest that in this specific case, A. butzleri was the etiological agent. Further investigations are needed to develop standardized diagnostic protocols and to establish the prevalence and significance of Aliarcobacter infections in humans.

RND Efflux Systems Contribute to Resistance and Virulence of Aliarcobacter butzleri

Aliarcobacter butzleri is an emergent enteropathogen that can be found in a range of environments. This bacterium presents a vast repertoire of efflux pumps, such as the ones belonging to the resistance nodulation cell division family, which may be associated with bacterial resistance, as well as virulence. Thus, this work aimed to evaluate the contribution of three RND efflux systems, AreABC, AreDEF and AreGHI, in the resistance and virulence of A. butzleri. Mutant strains were constructed by inactivation of the gene that encodes the inner membrane protein of these systems. The bacterial resistance profile of parental and mutant strains to several antimicrobials was assessed, as was the intracellular accumulation of the ethidium bromide dye. Regarding bacterial virulence, the role of these three efflux pumps on growth, strain fitness, motility, biofilm formation ability, survival in adverse conditions (oxidative stress and bile salts) and human serum and in vitro adhesion and invasion to Caco-2 cells was evaluated. We observed that the mutants from the three efflux pumps were more susceptible to several classes of antimicrobials than the parental strain and presented an increase in the accumulation of ethidium bromide, indicating a potential role of the efflux pumps in the extrusion of antimicrobials. The mutant strains had no bacterial growth defects; nonetheless, they presented a reduction in relative fitness. For the three mutants, an increase in the susceptibility to oxidative stress was observed, while only the mutant for AreGHI efflux pump showed a relevant role in bile stress survival. All the mutant strains showed an impairment in biofilm formation ability, were more susceptible to human serum and were less adherent to intestinal epithelial cells. Overall, the results support the contribution of the efflux pumps AreABC, AreDEF and AreGHI of A. butzleri to antimicrobial resistance, as well as to bacterial virulence.

Functional pangenome analysis reveals high virulence plasticity of Aliarcobacter butzleri and affinity to human mucus

Aliarcobacter butzleri is an emerging pathogen that may cause enteritis in humans, however, the incidence of disease caused by this member of the Campylobacteriaceae family is still underestimated. Furthermore, little is known about the precise virulence mechanism and behavior during infection. Therefore, in the present study, through complementary use of comparative genomics and physiological tests on human gut models, we sought to elucidate the genetic background of a set of 32 A. butzleri strains of diverse origin and to explore the correlation with the ability to colonize and invade human intestinal cells in vitro. The simulated infection of human intestinal models showed a higher colonization rate in presence of mucus-producing cells. For some strains, human mucus significantly improved the resistance to physical removal from the in vitro mucosa, while short time-frame growth was even observed. Pangenome analysis highlighted a hypervariable accessory genome, not strictly correlated to the isolation source. Likewise, the strain phylogeny was unrelated to their shared origin, despite a certain degree of segregation was observed among strains isolated from different segments of the intestinal tract of pigs. The putative virulence genes detected in all strains were mostly encompassed in the accessory fraction of the pangenome. The LPS biosynthesis and in particular the chain glycosylation of the O-antigen is harbored in a region of high plasticity of the pangenome, which would indicate frequent horizontal gene transfer phenomena, as well as the involvement of this hypervariable structure in the adaptive behavior and sympatric evolution of A. butzleri. Results of the present study deepen the current knowledge on A. butzleri pangenome by extending the pool of genes regarded as virulence markers and provide bases to develop new diagnostic approaches for the detection of those strains with a higher virulence potential.

Aliarcobacter butzleri from Water Poultry: Insights into Antimicrobial Resistance, Virulence and Heavy Metal Resistance

Aliarcobacter butzleri is the most prevalent Aliarcobacter species and has been isolated from a wide variety of sources. This species is an emerging foodborne and zoonotic pathogen because the bacteria can be transmitted by contaminated food or water and can cause acute enteritis in humans. Currently, there is no database to identify antimicrobial/heavy metal resistance and virulence-associated genes specific for A. butzleri. The aim of this study was to investigate the antimicrobial susceptibility and resistance profile of two A. butzleri isolates from Muscovy ducks (Cairina moschata) reared on a water poultry farm in Thuringia, Germany, and to create a database to fill this capability gap. The taxonomic classification revealed that the isolates belong to the Aliarcobacter gen. nov. as A. butzleri comb. nov. The antibiotic susceptibility was determined using the gradient strip method. While one of the isolates was resistant to five antibiotics, the other isolate was resistant to only two antibiotics. The presence of antimicrobial/heavy metal resistance genes and virulence determinants was determined using two custom-made databases. The custom-made databases identified a large repertoire of potential resistance and virulence-associated genes. This study provides the first resistance and virulence determinants database for A. butzleri.