Arcobacter halophilus sp. nov., the first obligate halophile in the genus Arcobacter

Illegal dumping of oil and gas wastewater alters arid soil microbial communities

The Permian Basin, underlying southeast New Mexico and west Texas, is one of the most productive oil and gas (OG) provinces in the United States. Oil and gas production yields large volumes of wastewater with complex chemistries, and the environmental health risks posed by these OG wastewaters on sensitive desert ecosystems are poorly understood. Starting in November 2017, 39 illegal dumps, as defined by federal and state regulations, of OG wastewater were identified in southeastern New Mexico, releasing ~600,000 L of fluid onto dryland soils. To evaluate the impacts of these releases, we analyzed changes in soil geochemistry and microbial community composition by comparing soils from within OG wastewater dump-affected samples to unaffected zones. We observed significant changes in soil geochemistry for all dump-affected compared with control samples, reflecting the residual salts and hydrocarbons from the OG-wastewater release (e.g., enriched in sodium, chloride, and bromide). Microbial community structure significantly (P < 0.01) differed between dump and control zones, with soils from dump areas having significantly (P < 0.01) lower alpha diversity and differences in phylogenetic composition. Dump-affected soil samples showed an increase in halophilic and halotolerant taxa, including members of the Marinobacteraceae, Halomonadaceae, and Halobacteroidaceae, suggesting that the high salinity of the dumped OG wastewater was exerting a strong selective pressure on microbial community structure. Taxa with high similarity to known hydrocarbon-degrading organisms were also detected in the dump-affected soil samples. Overall, this study demonstrates the potential for OG wastewater exposure to change the geochemistry and microbial community dynamics of arid soils.IMPORTANCEThe long-term environmental health impacts resulting from releases of oil and gas (OG) wastewater, typically brines with varying compositions of ions, hydrocarbons, and other constituents, are understudied. This is especially true for sensitive desert ecosystems, where soil microbes are key primary producers and drivers of nutrient cycling. We found that releases of OG wastewater can lead to shifts in microbial community composition and function toward salt- and hydrocarbon-tolerant taxa that are not typically found in desert soils, thus altering the impacted dryland soil ecosystem. Loss of key microbial taxa, such as those that catalyze organic carbon cycling, increase arid soil fertility, promote plant health, and affect soil moisture retention, could result in cascading effects across the sensitive desert ecosystem. By characterizing environmental changes due to releases of OG wastewater to soils overlying the Permian Basin, we gain further insights into how OG wastewater may alter dryland soil microbial functions and ecosystems.

Chitinophaga pendula, sp. nov., from an air conditioner condensate drain line

A Gram-negative, rod-shaped and filamentous bacterium designated MD30BT was isolated from a biofilm hanging in water flowing from an air conditioner condensate drain line in Honolulu, Hawai'i. Based on 1517 nucleotides of the strain's 16S rRNA gene, its nearest neighbours are Chitinophaga rhizosphaerae T16R-86T (96.7 %), Chitinophaga caseinilytica S-52T (96.6 %), Chitinophaga lutea ZY74T (96.6 %), Chitinophaga niabensis JS13-10T (96.6 %) and Chitinophaga ginsengisoli Gsoil 052T (96.5 %). MD30BT cells are non-motile, strictly aerobic, and catalase and oxidase positive. Growth occurs between 10 and 45 °C. Major fatty acids in whole cells of MD30BT are 13-methyl tetradecanoic acid (34.1 %), cis-11-hexadecenoic acid (30.3 %), and 3-hydroxy, 15-methyl hexadecanoic acid (13.3 %). The quinone system contains predominantly menaquinone MK-7. The polar lipid profile contains the major lipids phosphatidylethanolamine, one unidentified lipid lacking a functional group, and two unidentified aminolipids. sym-Homospermidine is the major polyamine. The G+C content of the genome is 47.58 mol%. Based on phenotypic and genotypic differences between MD30BT and extant species in the Chitinophaga, we propose that MD30BT represents a new Chitinophaga species, for which the name Chitinophaga pendula sp. nov. is proposed to accommodate strain MD30BT as the type strain (DSM 112477T=NCTC 14606T).

Genotyping, antibiotic resistance and prevalence of Arcobacter species in milk and dairy products

BACKGROUND

Arcobacter spp. has been considered an emerging foodborne pathogen and a hazard to human health. The dairy chain has been isolated from different sources; nevertheless, data on Arcobacter occurrence in raw milk and dairy products in Iran are still scant.

OBJECTIVE

The present study investigates the prevalence, antimicrobial susceptibility and the presence of virulence genes of Arcobacters species isolated from milk and dairy products.

METHODS

Then, a total of 350 raw milk samples and 400 dairy product samples were collected from dairy supply centers in Isfahan, Iran. Presumptive Arcobacter strains were obtained by enriching samples in Oxoid Arcobacter enrichment broth (AEB) followed by the filtration of enrichment product through 0.45-μm pore size membrane filters laid onto non-selective blood at 30°C under microaerophilic conditions. Molecular identification of Arcobacter cryaerophilus and A. butzleri was performed by Polymerase chain reaction (PCR) amplification of the 16S rRNA gene, followed by sequencing. The disc diffusion method was used to determine the antimicrobial susceptibility of isolates. Targeted resistance and virulence genes were detected using multiplex PCR.

RESULTS

The results show a low recovery rate of Arcobacter spp. in milk. Arcobacters were found in all types of milk, except raw camel milk, but were absent from all dairy products. Arcobacter butzleri was the predominant species in raw milk. Detection of virulence genes shows that all virulence genes targeted were found among A. butzleri, and six (cadF, cj1349, irgA, mviN, pldA, tlyA) were found among A. cryaerophilus. All A. butzleri strains and some A. cryaerophilus strains isolated from milk were resistant to amoxicillin-clavulanic acid and tetracycline. All A. cryaerophilus isolates from milk were susceptible to gentamycin, streptomycin, erythromycin and ciprofloxacin. The distribution of resistance genes in Arcobacter strains in milk shows that all isolates carried tet(O) and bla_OXA-61 genes.

CONCLUSIONS

In conclusion, the results indicate a low recovery rate of Arcobacter spp. in milk and milk products. However, a significant number of Arcobacter strains with putative virulence genes may be potential pathogens for humans and an overall increase in Arcobacter resistance to first-line antibiotics. These results highlight the need for regular surveillance of Arcobacter strains in milk and milk products in Iran.

A Review on the Prevalence of Arcobacter in Aquatic Environments

Arcobacter is an emerging pathogen that is associated with human and animal diseases. Since its first introduction in 1991, 33 Arcobacter species have been identified. Studies have reported that with the presence of Arcobacter in environmental water bodies, animals, and humans, a possibility of its transmission via water and food makes it a potential waterborne and foodborne pathogen. Therefore, this review article focuses on the general characteristics of Arcobacter, including its pathogenicity, antimicrobial resistance, methods of detection by cultivation and molecular techniques, and its presence in water, fecal samples, and animal products worldwide. These detection methods include conventional culture methods, and rapid and accurate Arcobacter identification at the species level, using quantitative polymerase chain reaction (qPCR) and multiplex PCR. Arcobacter has been identified worldwide from feces of various hosts, such as humans, cattle, pigs, sheep, horses, dogs, poultry, and swine, and also from meat, dairy products, carcasses, buccal cavity, and cloacal swabs. Furthermore, Arcobacter has been detected in groundwater, river water, wastewater (influent and effluent), canals, treated drinking water, spring water, and seawater. Hence, we propose that understanding the prevalence of Arcobacter in environmental water and fecal-source samples and its infection of humans and animals will contribute to a better strategy to control and prevent the survival and growth of the bacteria.

Arcobacter vandammei sp. nov., isolated from the rectal mucus of a healthy pig

A study on the polyphasic taxonomic classification of an Arcobacter strain, R-73987^T, isolated from the rectal mucus of a porcine intestinal tract, was performed. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain could be assigned to the genus Arcobacter and suggested that strain R-73987^T belongs to a novel undescribed species. Comparative analysis of the rpoB gene sequence confirmed the findings. Arcobacter faecis LMG 28519^T was identified as its closest neighbour in a multigene analysis based on 107 protein- encoding genes. Further, whole-genome sequence comparisons by means of average nucleotide identity and in silico DNA-DNA hybridization between the genome of strain R-73987^T and the genomes of validly named Arcobacter species resulted in values below 95-96 and 70  %, respectively. In addition, a phenotypic analysis further corroborated the conclusion that strain R-73987^T represents a novel Arcobacter species, for which the name Arcobacter vandammei sp. nov. is proposed. The type strain is R-73987^T (=LMG 31429^T=CCUG 75005^T). This appears to be the first Arcobacter species recovered from porcine intestinal mucus.

Influence of metabolic cosubstrates on methanogenic potential and degradation of triclosan and propranolol in sanitary sewage

Triclosan (TCS) and propranolol (PRO) are emerging micropollutants that are difficult to remove in wastewater treatment plants. In this study, methanogenic potential (P) of anaerobic sludge submitted to TCS (3.6 ± 0.1 to 15.5 ± 0.1 mg L^-1) and PRO (6.1 ± 0.1 to 55.9 ± 1.2 mg L^-1) in sanitary sewage, was investigated in batch reactors. The use of cosubstrates (200 mg L^-1 of organic matter) ethanol, methanol:ethanol and fumarate was evaluated for micropollutant degradation. Without cosubstrates, P values for 5.0 ± 0.1 mgTCS L^-1, 15.5 ± 0.1 mgTCS L^-1 and 55.0 ± 1.3 mgPRO L^-1 were 50.53%, 98.24% and 17.66% lower in relation to Control assay (855 ± 5 μmolCH4) with sanitary sewage, without micropollutants and cosubstrates, respectively. The use of fumarate, ethanol and methanol:ethanol favored greater methane production, with P values of 2144 ± 45 μmolCH₄, 2960 ± 185 μmolCH₄ and 2239 ± 171 μmolCH₄ for 5.1 ± 0.1 mgTCS L^-1, respectively; and of 10,827 ± 185 μmolCH₄, 10,946 ± 108 μmolCH₄ and 10,809 ± 210 μmolCH₄ for 55.0 ± 1.3 mgPRO L^-1, respectively. Greater degradation of TCS (77.1 ± 0.1% for 5.1 ± 0.1 mg L^-1) and PRO (24.1 ± 0.1% for 55.9 ± 1.2 mg L^-1) was obtained with ethanol. However, with 28.5 ± 0.5 mg PRO L^-1, greater degradation (88.4 ± 0.9%) was obtained without cosubstrates. With TCS, via sequencing of rRNA 16S gene, for Bacteria Domain, greater abundance of phylum Chloroflexi and of the genera Longilinea, Arcobacter, Mesotoga and Sulfuricurvum were identified. With PRO, the genus VadinBC27 was the most abundant. Methanosaeta was dominant in TCS with ethanol, while in PRO without cosubstrates, Methanobacterium and Methanosaeta were the most abundant. The use of metabolic cosubstrates is a favorable strategy to obtain greater methanogenic potential and degradation of TCS and PRO.

Exploring the allochthonous pollution influence on bacterial community and co-occurrence dynamics of River Ganga water through 16S rRNA-tagged amplicon metagenome

River Ganga is one of the largest and most sacred rivers of India. This river is largely affected by anthropogenic activities causing significant increase in water pollution. The impact of drains discharging polluted water on the bacterial community dynamics in the river remains unexplored. To elucidate this, the targeted 16S rRNA V3-V4 variable region amplicon sequencing and bioinformatic analysis were performed using water from upstream, drain, and downstream of river Ganga. Analysis revealed significant difference in relative abundances of bacterial communities. The increase in bacterial abundance and alpha diversity was detected in the downstream compared to the upstream. Environmental factors were found significantly different between upstream and downstream water. At the phyla level, highly abundant taxa such as Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Verrucomicrobia were observed. Bacterial genera like Prevotella, Bacteroides, Blautia, and Faecalibacterium (fecal indicator) had higher abundance in the downstream site. Network co-occurrence revealed that bacterial communities have a modular profile with reduced interaction in drain and downstream water. The network of co-occurring bacterial communities consists of 283 nodes with edge connectivity of 6900, 7074, and 5294 in upstream, drain, and downstream samples, respectively. Upstream communities exhibited the highest positive interaction followed by the drain and the downstream sites. Additionally, highly abundant pathogenic species such as Acinetobacter baumannii and Prevotella copri were also detected in all samples. This study suggests the drain to be allochthonous pollution vector that significantly contributes to bacterial community enrichment. From the results of this study, it is apparent that the lotic water may be used as the ecological reference to understand and monitor the variations in the bacterial communities and their co-occurrence dynamics in the fresh water ecosystems.

The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment

The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique inland salt marsh environment.

Improved culture enrichment broth for isolation of Arcobacter-like species from the marine environment

Arcobacter-like species are found associated with many matrices, including shellfish in marine environments. The culture media and conditions play a major role in the recovery of new Arcobacter-like species. This study was aimed to develop a culture media for isolation and enhanced growth of Arcobacter-like spp. from marine and shellfish matrices. For this purpose, 14 different Arcobacter-like spp. mostly isolated from shellfish, were grown in 24 different formulations of enrichment broths. The enrichment broths consisted of five main groups based on the organic contents (fresh oyster homogenate, lyophilized oyster either alone or in combination with other standard media), combined with artificial seawater (ASW) or 2.5% NaCl. Optical density (OD_420nm) measurements after every 24 h were compared with the growth in control media (Arcobacter broth) in parallel. The mean and standard deviation were calculated for each species in each broth and statistical differences (p < 0.05) among broths were calculated by ANOVA. The results indicated that shellfish-associated Arcobacter-like species growth was significantly higher in Arcobacter broth + 50% ASW and the same media supplemented with lyophilized oysters. This is the first study to have used fresh or lyophilized oyster flesh in the enrichment broth for isolation of shellfish-associated Arcobacter-like spp.

Complete Genome Sequencing of Four Arcobacter Species Reveals a Diverse Suite of Mobile Elements

Arcobacter species are recovered from a wide variety of sources, including animals, food, and both fresh and marine waters. Several Arcobacter species have also been recovered from human clinical samples and are thus associated tentatively with food- and water-borne human illnesses. Genome sequencing of the poultry isolate Arcobacter cibarius H743 and the Arcobacter acticola, Arcobacter pacificus, and Arcobacter porcinus type strains identified a large number and variety of insertion sequences. This study presents an analysis of these A. acticola, A. cibarius, A. pacificus, and A. porcinus IS elements. The four genomes sequenced here contain 276 complete and degenerate IS elements, representing 13 of the current 29 prokaryotic IS element families. Expansion of the analysis to include 15 other previously sequenced Arcobacter spp. added 73 complete and degenerate IS elements. Several of these IS elements were identified in two or more Arcobacter species, suggesting movement by horizontal gene transfer between the arcobacters. These IS elements are putatively associated with intragenomic deletions and inversions, and tentative movement of antimicrobial resistance genes. The A. cibarius strain H743 megaplasmid contains multiple IS elements common to the chromosome and, unusually, a complete ribosomal RNA locus, indicating that larger scale genomic rearrangements, potentially resulting from IS element-mediated megaplasmid cointegration and resolution may be occurring within A. cibarius and possibly other arcobacters. The presence of such a large and varied suite of mobile elements could have profound effects on Arcobacter biology and evolution.

Diversity, enumeration, and isolation of Arcobacter spp. in the giant abalone, Haliotis gigantea

Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery resource. This study aimed to investigate the genetic diversity and abundance of bacteria from the genus Arcobacter in the Japanese giant abalone, Haliotis gigantea, using molecular methods such as Arcobacter‐specific clone libraries and fluorescence in situ hybridization (FISH). Furthermore, we attempted to isolate the Arcobacter species detected. Twelve genotypes of clones were obtained from Arcobacter‐specific clone libraries. These sequences are not classified with any other known Arcobacter species including pathogenic Arcobacter spp., A. butzleri, A. skirrowii, and A. cryaerophilus, commonly isolated or detected from bivalves. From the FISH analysis, we observed that ARC94F‐positive cells, presumed to be Arcobacter, accounted for 6.96 ± 0.72% of all EUB338‐positive cells. In the culture method, three genotypes of Arcobacter were isolated from abalones. One genotype had a similarity of 99.2%–100.0% to the 16S rRNA gene of Arcobacter marinus, while the others showed only 93.3%–94.3% similarity to other Arcobacter species. These data indicate that abalones carry Arcobacter as a common bacterial genus which includes uncultured species.

Living in Cold Blood: Arcobacter, Campylobacter, and Helicobacter in Reptiles

Species of the Epsilonproteobacteria genera Arcobacter, Campylobacter, and Helicobacter are commonly associated with vertebrate hosts and some are considered significant pathogens. Vertebrate-associated Epsilonproteobacteria are often considered to be largely confined to endothermic mammals and birds. Recent studies have shown that ectothermic reptiles display a distinct and largely unique Epsilonproteobacteria community, including taxa which can cause disease in humans. Several Arcobacter taxa are widespread amongst reptiles and often show a broad host range. Reptiles carry a large diversity of unique and novel Helicobacter taxa, which apparently evolved in an ectothermic host. Some species, such as Campylobacter fetus, display a distinct intraspecies host dichotomy, with genetically divergent lineages occurring either in mammals or reptiles. These taxa can provide valuable insights in host adaptation and co-evolution between symbiont and host. Here, we present an overview of the biodiversity, ecology, epidemiology, and evolution of reptile-associated Epsilonproteobacteria from a broader vertebrate host perspective.

Complete Genome Sequence of the Arcobacter halophilus Type Strain CCUG 53805

Many Arcobacter spp. are free living and are routinely recovered from marine environments.

Many Arcobacter spp. are free living and are routinely recovered from marine environments. Arcobacter halophilus was isolated from hypersaline lagoon water in the Hawaiian islands, and it was demonstrated to be an obligate halophile. This study describes the complete whole-genome sequence of the A. halophilus type strain, CCUG 53805 (= LA31B^T = ATCC BAA-1022^T).

Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin

Hydraulic fracturing is the prevailing method for enhancing recovery of hydrocarbon resources from unconventional shale formations, yet little is understood regarding the microbial impact on biogeochemical cycling in natural-gas wells. Although the metabolisms of certain fermentative bacteria and methanogenic archaea that dominate in later produced fluids have been well studied, few details have been reported on microorganisms prevelant during the early flowback period, when oxygen and other surface-derived oxyanions and nutrients become depleted. Here, we report the isolation, genomic and phenotypic characterization of Marinobacter and Arcobacter bacterial species from natural-gas wells in the Utica-Point Pleasant and Marcellus Formations coupled to supporting geochemical and metagenomic analyses of produced fluid samples. These unconventional hydrocarbon system-derived Marinobacter sp. are capable of utilizing a diversity of organic carbon sources including aliphatic and aromatic hydrocarbons, amino acids, and carboxylic acids. Marinobacter and Arcobacter can metabolize organic nitrogen sources and have the capacity for denitrification and dissimilatory nitrate reduction to ammonia (DNRA) respectively; with DNRA and ammonification processes partially explaining high concentrations of ammonia measured in produced fluids. Arcobacter is capable of chemosynthetic sulfur oxidation, which could fuel metabolic processes for other heterotrophic, fermentative, or sulfate-reducing community members. Our analysis revealed mechanisms for growth of these taxa across a broad range of salinities (up to 15% salt), which explains their enrichment during early natural-gas production. These results demonstrate the prevalence of Marinobacter and Arcobacter during a key maturation phase of hydraulically fractured natural-gas wells, and highlight the significant role these genera play in biogeochemical cycling for this economically important energy system.

Complete Genome Sequence of the Arcobacter marinus Type Strain JCM 15502

Arcobacter species are often recovered from marine environments and are isolated from both seawater and shellfish. Arcobacter marinus was recovered from the homogenate of a sample containing surface seawater, seaweed, and a starfish. This study describes the whole-genome sequence of the A. marinus type strain JCM 15502 (= CL-S1T = KCCM 90072T).

Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos

Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposed.

A Polyphasic and Taxogenomic Evaluation Uncovers Arcobacter cryaerophilus as a Species Complex That Embraces Four Genomovars

The species Arcobacter cryaerophilus is found in many food products of animal origin and is the dominating species in wastewater. In addition, it is associated with cases of farm animal and human infectious diseases,. The species embraces two subgroups i.e., 1A (LMG 24291^T = LMG 9904^T) and 1B (LMG 10829) that can be differentiated by their 16S rRNA-RFLP pattern. However, some authors, on the basis of the shared intermediate levels of DNA-DNA hybridization, have suggested abandoning the subgroup classification. This contradiction indicates that the taxonomy of this species is not yet resolved. The objective of the present study was to perform a taxonomic evaluation of the diversity of A. cryaerophilus. Genomic information was used along with a Multilocus Phylogenetic Analysis (MLPA) and phenotypic characterization on a group of 52 temporally and geographically dispersed strains, coming from different types of samples and hosts from nine countries. The MLPA analysis showed that those strains formed four clusters (I–IV). Values of Average Nucleotide Identity (ANI) and in silico DNA-DNA Hybridization (isDDH) obtained between 13 genomes representing strains of the four clusters were below the proposed cut-offs of 96 and 70%, respectively, confirming that each of the clusters represented a different genomic species. However, none of the evaluated phenotypic tests enabled their unequivocal differentiation into species. Therefore, the genomic delimited clusters should be considered genomovars of the species A. cryaerophilus. These genomovars could have different clinical importance, since only the cluster I included strains isolated from human specimens. The discovery of at least one stable distinctive phenotypic character would be needed to define each cluster or genomovar as a different species. Until then, we propose naming them “A. cryaerophilus gv. pseudocryaerophilus” (Cluster I = LMG 10229^T), “A. cryaerophilus gv. crypticus” (Cluster II = LMG 9065^T), “A. cryaerophilus gv. cryaerophilus” (Cluster III = LMG 24291^T) and “A. cryaerophilus gv. occultus” (Cluster IV = LMG 29976^T).

Isolation and molecular characterization of Arcobacter butzleri and Arcobacter cryaerophilus from the pork production chain in Brazil

ABSTRACT: Arcobacter is an emerging zoonotic pathogen, and the major transmission routes to humans are the handling or consumption of contaminated raw/undercooked food products of animal origin, water and seafood. The isolation and identification of Arcobacter species are not routine in clinical laboratories; therefore, its true incidence in human infections may be underestimated. The present study aimed to isolate and characterize Arcobacter from carcasses and fecal samples collected at swine slaughterhouses and from meat markets in São Paulo State, Brazil. The isolates were identified using multiplex-PCR to differentiate the species and analyzed by single-enzyme amplified fragment length polymorphism (SE-AFLP). Arcobacter spp. were isolated from 73.0% of swine carcasses, 4% of fecal samples and 10% of pork samples. A. butzleri was the most prevalent species identified, followed by A. cryaerophilus. Interestingly, the carcasses presented higher frequency of A. butzleri isolation, whereas only A. cryaerophilus was isolated from fecal samples. SE-AFLP enabled the characterization of A. butzleri and A. cryaerophilus into 51 and 63 profiles, respectively. The great genetic heterogeneity observed for both species corroborates previous reports. This study confirms the necessity for a standard isolation protocol and the improvement of molecular tools to further elucidate Arcobacter epidemiology.

Arcobacter canalis sp. nov., isolated from a water canal contaminated with urban sewage

Four bacterial strains recovered from shellfish (n=3) and from the water (n=1) of a canal contaminated with urban sewage were recognized as belonging to a novel species of the genus Arcobacter (represented by strain F138-33^T) by using a polyphasic characterization. All the new isolates required 2 % NaCl to grow. Phylogenetic analyses based on 16S rRNA gene sequences indicated that all strains clustered together, with the most closely related species being Arcobacter marinus and Arcobactermolluscorum. However, phylogenetic analyses using the concatenated sequences of housekeeping genes (atpA, gyrB, hsp60, gyrA and rpoB) showed that all the novel strains formed a distinct lineage within the genus Arcobacter. Results of in silico DNA-DNA hybridization and the average nucleotide identity between the genome of strain F138-33^T and those of the closely related species A. marinus and other relatively closely related species such as A. molluscorum and Arcobacterhalophilus were all below 70 and 96 %, respectively. All the above results, together with the 15 physiological and biochemical tests that could distinguish the newly isolated strains from the closely related species, confirmed that these strains represent a novel species for which the name Arcobacter canalis sp. nov. is proposed, with the type strain F138-33^T (=CECT 8984^T=LMG 29148^T).

Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control - a comprehensive review

Arcobacter has emerged as an important food-borne zoonotic pathogen, causing sometimes serious infections in humans and animals. Newer species of Arcobacter are being incessantly emerging (presently 25 species have been identified) with novel information on the evolutionary mechanisms and genetic diversity among different Arcobacter species. These have been reported from chickens, domestic animals (cattle, pigs, sheep, horses, dogs), reptiles (lizards, snakes and chelonians), meat (poultry, pork, goat, lamb, beef, rabbit), vegetables and from humans in different countries. Arcobacters are implicated as causative agents of diarrhea, mastitis and abortion in animals, while causing bacteremia, endocarditis, peritonitis, gastroenteritis and diarrhea in humans. Three species including A. butzleri, A. cryaerophilus and A. skirrowii are predominantly associated with clinical conditions. Arcobacters are primarily transmitted through contaminated food and water sources. Identification of Arcobacter by biochemical tests is difficult and isolation remains the gold standard method. Current diagnostic advances have provided various molecular methods for efficient detection and differentiation of the Arcobacters at genus and species level. To overcome the emerging antibiotic resistance problem there is an essential need to explore the potential of novel and alternative therapies. Strengthening of the diagnostic aspects is also suggested as in most cases Arcobacters goes unnoticed and hence the exact epidemiological status remains uncertain. This review updates the current knowledge and many aspects of this important food-borne pathogen, namely etiology, evolution and emergence, genetic diversity, epidemiology, the disease in animals and humans, public health concerns, and advances in its diagnosis, prevention and control.

Minimal standards for describing new species belonging to the families Campylobacteraceae and Helicobacteraceae: Campylobacter, Arcobacter, Helicobacter and Wolinella spp

Ongoing changes in taxonomic methods, and in the rapid development of the taxonomic structure of species assigned to the Epsilonproteobacteria have lead the International Committee of Systematic Bacteriology Subcommittee on the Taxonomy of Campylobacter and Related Bacteria to discuss significant updates to previous minimal standards for describing new species of Campylobacteraceae and Helicobacteraceae. This paper is the result of these discussions and proposes minimum requirements for the description of new species belonging to the families Campylobacteraceae and Helicobacteraceae, thus including species in Campylobacter, Arcobacter, Helicobacter, and Wolinella. The core underlying principle remains the use of appropriate phenotypic and genotypic methods to characterise strains sufficiently so as to effectively and unambiguously determine their taxonomic position in these families, and provide adequate means by which the new taxon can be distinguished from extant species and subspecies. This polyphasic taxonomic approach demands the use of appropriate reference data for comparison to ensure the novelty of proposed new taxa, and the recommended study of at least five strains to enable species diversity to be assessed. Methodological approaches for phenotypic and genotypic (including whole-genome sequence comparisons) characterisation are recommended.

Arcobacter haliotis sp. nov., isolated from abalone species Haliotis gigantea

A Gram-negative, aerobic, polar-flagellated and rod-shaped, sometimes slightly curved bacterium, designated MA5T, was isolated from the gut of an abalone of the species Haliotis gigantea collected in Japan. Phylogenetic analyses based on 16S rRNA, gyrB, hsp60 and rpoB gene sequences placed strain MA5T in the genus Arcobacter in an independent phylogenetic line. Comparison of the 16S rRNA gene sequence of this strain with those of the type strains of the established Arcobacter species revealed A. nitrofigilis (95.1 %) as nearest neighbour. Strain MA5T grew optimally at 25 °C, pH 6.0 to 9.0 and in the presence of 2 to 5 % (w/v) NaCl under both aerobic and microaerobic conditions. The predominant fatty acids found were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c), C12 : 0 3-OH and C18 : 1 ω7c. Menaquinone-6 (MK-6) and menaquinone-7 (MK-7) were found as the major respiratory quinones. The major polar lipids detected were phosphatidylethanolamine and phosphatidylglycerol. Strain MA5T could be differentiated phenotypically from the phylogenetic closest Arcobacter species by its ability to grow on 0.05 % safranin and 0.01 % 2,3,5-triphenyl tetrazolium chloride (TTC), but not on 0.5 % NaCl. The obtained DNA G+C content of strain MA5T was 27.9 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic distinctiveness of MA5T, this strain is considered to represent a novel species of the genus Arcobacter, for which the name Arcobacter haliotis sp. nov. is proposed. The type strain is MA5T (=LMG 28652T=JCM 31147T).

Arcobacter lekithochrous sp. nov., isolated from a molluscan hatchery

Four bacterial strains, LFT 1.7T, LT2C 2.5, LT4C 2.8 and TM 4.6, were isolated from great scallop (Pecten maximus) larvae and tank seawater in a Norwegian hatchery and characterized by a polyphasic approach including determination of phenotypic, chemotaxonomic and genomic traits. All were Gram-stain-negative, motile rods, oxidase- and catalase-positive and required sea salts for growth. Major fatty acids present were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), summed feature 8 (C18 : 1ω7c or C18 : 1ω6c), C16 : 0, C14 : 0, summed feature 2 (C14 : 0 3-OH/iso-C16 : 1 I), C12 : 0 3-OH and C12 : 0. Strain LFT 1.7T contained menaquinone MK-6 as the sole respiratory quinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that all strains formed a distinct lineage within the genus Arcobacter with a low similarity to known species (94.77-95.32 %). The DNA G+C content was 28.7 mol%. Results of in silico DNA-DNA hybridization and average nucleotide identity confirmed that the isolates constitute a novel species of Arcobacter, for which the name Arcobacter lekithochrous sp. nov. is proposed. The type strain is LFT 1.7T (=CECT 8942T=DSM 100870T).

Impact of Seasonal Hypoxia on Activity and Community Structure of Chemolithoautotrophic Bacteria in a Coastal Sediment

Seasonal hypoxia in coastal systems drastically changes the availability of electron acceptors in bottom water, which alters the sedimentary reoxidation of reduced compounds. However, the effect of seasonal hypoxia on the chemolithoautotrophic community that catalyzes these reoxidation reactions is rarely studied. Here, we examine the changes in activity and structure of the sedimentary chemolithoautotrophic bacterial community of a seasonally hypoxic saline basin under oxic (spring) and hypoxic (summer) conditions. Combined 16S rRNA gene amplicon sequencing and analysis of phospholipid-derived fatty acids indicated a major temporal shift in community structure. Aerobic sulfur-oxidizing Gammaproteobacteria (Thiotrichales) and Epsilonproteobacteria (Campylobacterales) were prevalent during spring, whereas Deltaproteobacteria (Desulfobacterales) related to sulfate-reducing bacteria prevailed during summer hypoxia. Chemolithoautotrophy rates in the surface sediment were three times higher in spring than in summer. The depth distribution of chemolithoautotrophy was linked to the distinct sulfur oxidation mechanisms identified through microsensor profiling, i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae The metabolic diversity of the sulfur-oxidizing bacterial community suggests a complex niche partitioning within the sediment, probably driven by the availability of reduced sulfur compounds (H₂S, S⁰, and S₂O₃^2-) and electron acceptors (O₂ and NO₃^-) regulated by seasonal hypoxia.IMPORTANCE Chemolithoautotrophic microbes in the seafloor are dependent on electron acceptors, like oxygen and nitrate, that diffuse from the overlying water. Seasonal hypoxia, however, drastically changes the availability of these electron acceptors in the bottom water; hence, one expects a strong impact of seasonal hypoxia on sedimentary chemolithoautotrophy. A multidisciplinary investigation of the sediments in a seasonally hypoxic coastal basin confirms this hypothesis. Our data show that bacterial community structure and chemolithoautotrophic activity varied with the seasonal depletion of oxygen. Unexpectedly, the dark carbon fixation was also dependent on the dominant microbial pathway of sulfur oxidation occurring in the sediment (i.e., canonical sulfur oxidation, electrogenic sulfur oxidation by cable bacteria, and sulfide oxidation coupled to nitrate reduction by Beggiatoaceae). These results suggest that a complex niche partitioning within the sulfur-oxidizing bacterial community additionally affects the chemolithoautotrophic community of seasonally hypoxic sediments.

Enhanced recovery of Arcobacter spp. using NaCl in culture media and re-assessment of the traits of Arcobacter marinus and Arcobacter halophilus isolated from marine water and shellfish

The genus Arcobacter is a relatively poorly known group of bacteria, and the number of new species and sequences from non-culturable strains has increased considerably in recent years. This study investigates whether using media that contain NaCl might help to improve the recovery of Arcobacter spp. from marine environments. To this aim, 62 water and shellfish samples were analysed in parallel, with both a commonly used culture method (enrichment in Arcobacter-CAT broth followed by culture on Blood Agar) and a new one that supplements the Arcobacter-CAT enrichment broth with 2.5% NaCl (w/v) followed by culturing on Marine Agar. The new method yielded ca. 40% more positive samples and provided a higher diversity of known (11 vs. 7) and unknown (7 vs. 2) Arcobacter species. Among the 11 known species recovered, Arcobacter marinus and Arcobacter halophilus were isolated only by this new method. No more strains of these species have been isolated since their original descriptions, both of which were based only on a single strain. In view of that, the phenotypic characteristics of these species are re-evaluated in the present study, using the new strains. Strains of A. halophilus had the same phenotypic profile as the type strain. However, some strains of A. marinus differed from the type strain in that they did not hydrolyse indoxyl-acetate, becoming, therefore, the first Arcobacter species to show a varying ability to hydrolyse indoxyl-acetate. This study shows to what extent a simple variation to the culture media can have a big influence on positive samples and on the community of species recovered.

Spatial isolation and environmental factors drive distinct bacterial and archaeal communities in different types of petroleum reservoirs in China

To investigate the spatial distribution of microbial communities and their drivers in petroleum reservoir environments, we performed pyrosequencing of microbial partial 16S rRNA, derived from 20 geographically separated water-flooding reservoirs, and two reservoirs that had not been flooded, in China. The results indicated that distinct underground microbial communities inhabited the different reservoirs. Compared with the bacteria, archaeal alpha-diversity was not strongly correlated with the environmental variables. The variation of the bacterial and archaeal community compositions was affected synthetically, by the mining patterns, spatial isolation, reservoir temperature, salinity and pH of the formation brine. The environmental factors explained 64.22% and 78.26% of the total variance for the bacterial and archaeal communities, respectively. Despite the diverse community compositions, shared populations (48 bacterial and 18 archaeal genera) were found and were dominant in most of the oilfields. Potential indigenous microorganisms, including Carboxydibrachium, Thermosinus, and Neptunomonas, were only detected in a reservoir that had not been flooded with water. This study indicates that: 1) the environmental variation drives distinct microbial communities in different reservoirs; 2) compared with the archaea, the bacterial communities were highly heterogeneous within and among the reservoirs; and 3) despite the community variation, some microorganisms are dominant in multiple petroleum reservoirs.

Physiological and genomic characterization of Arcobacter anaerophilus IR-1 reveals new metabolic features in Epsilonproteobacteria

In this study we characterized and sequenced the genome of Arcobacter anaerophilus strain IR-1 isolated from enrichment cultures used in nitrate-amended corrosion experiments. A. anaerophilus IR-1 could grow lithoautotrophically on hydrogen and hydrogen sulfide and lithoheterothrophically on thiosulfate and elemental sulfur. In addition, the strain grew organoheterotrophically on yeast extract, peptone, and various organic acids. We show for the first time that Arcobacter could grow on the complex organic substrate tryptone and oxidize acetate with elemental sulfur as electron acceptor. Electron acceptors utilized by most Epsilonproteobacteria, such as oxygen, nitrate, and sulfur, were also used by A. anaerophilus IR-1. Strain IR-1 was also uniquely able to use iron citrate as electron acceptor. Comparative genomics of the Arcobacter strains A. butzleri RM4018, A. nitrofigilis CI and A. anaerophilus IR-1 revealed that the free-living strains had a wider metabolic range and more genes in common compared to the pathogen strain. The presence of genes for NAD(+)-reducing hydrogenase (hox) and dissimilatory iron reduction (fre) were unique for A. anaerophilus IR-1 among Epsilonproteobacteria. Finally, the new strain had an incomplete denitrification pathway where the end product was nitrite, which is different from other Arcobacter strains where the end product is ammonia. Altogether, our study shows that traditional characterization in combination with a modern genomics approach can expand our knowledge on free-living Arcobacter, and that this complementary approach could also provide invaluable knowledge about the physiology and metabolic pathways in other Epsilonproteobacteria from various environments.

Global Distribution and Prevalence of Arcobacter in Food and Water

The emerging foodborne and waterborne pathogen, Arcobacter, has been linked to various gastrointestinal diseases. Currently, 19 species are established or proposed; consequently, there has been an increase in the number of publications regarding Arcobacter since it was first introduced in 1991. To better understand the potential public health risks posed by Arcobacter, this review summarizes the current knowledge concerning the global distribution and the prevalence of Arcobacter in food and water. Arcobacter spp. were identified in food animals, food-processing environments and a variety of foods, including vegetables, poultry, beef, dairy products, seafood, pork, lamb and rabbit. A wide range of waterbodies has been reported to be contaminated with Arcobacter spp., such as wastewater, seawater, lake and river water, drinking water, groundwater and recreational water. In addition, Arcobacter has also been isolated from pets, domestic birds, wildlife, zoo and farm animals. It is expected that advancements in molecular techniques will facilitate better detection worldwide and aid in understanding the pathogenicity of Arcobacter. However, more extensive and rigorous surveillance systems are needed to better understand the occurrence of Arcobacter in food and water in various regions of the world, as well as uncover other potential public health risks, that is antibiotic resistance and disinfection efficiency, to reduce the possibility of foodborne and waterborne infections.

Insights in the pathogenesis and resistance of Arcobacter: A review

Arcobacter genus currently comprises 18 recognized species, among which Arcobacter butzleri, Arcobacter cryaerophilus and Arcobacter skirrowii have been associated with human and animal disease. Although these organisms, with special emphasis A. butzleri, are emerging as clinical pathogens, several aspects of their epidemiology and virulence are only starting to be clarified. In vitro human and animal cell culture assays have been used to show that several Arcobacter species can adhere to and invade eukaryotic cells, induce an immune response and produce toxins that damage host cells. In addition, data from genome sequencing highlighted several potential markers that may be helpful candidates for the study and understanding of these mechanisms; however, more work is necessary to clarify the molecular mechanisms involved in Arcobacter virulence. Arcobacter can be considered a relatively robust organism showing to be able to survive in adverse conditions, as the ones imposed by food processing and storage. Moreover, these bacteria have shown increased antibiotic resistance, along with high multidrug resistance. In this review, we seek to update the state-of-the-art concerning Arcobacter distribution, its interaction with the host, the trends of antibiotic resistance, its ability to survive, and finally the use of natural antimicrobials for control of Arcobacter.

Microbial carbon metabolism associated with electrogenic sulphur oxidation in coastal sediments

Recently, a novel electrogenic type of sulphur oxidation was documented in marine sediments, whereby filamentous cable bacteria (Desulfobulbaceae) are mediating electron transport over cm-scale distances. These cable bacteria are capable of developing an extensive network within days, implying a highly efficient carbon acquisition strategy. Presently, the carbon metabolism of cable bacteria is unknown, and hence we adopted a multidisciplinary approach to study the carbon substrate utilization of both cable bacteria and associated microbial community in sediment incubations. Fluorescence in situ hybridization showed rapid downward growth of cable bacteria, concomitant with high rates of electrogenic sulphur oxidation, as quantified by microelectrode profiling. We studied heterotrophy and autotrophy by following ¹³C-propionate and -bicarbonate incorporation into bacterial fatty acids. This biomarker analysis showed that propionate uptake was limited to fatty acid signatures typical for the genus Desulfobulbus. The nanoscale secondary ion mass spectrometry analysis confirmed heterotrophic rather than autotrophic growth of cable bacteria. Still, high bicarbonate uptake was observed in concert with the development of cable bacteria. Clone libraries of 16S complementary DNA showed numerous sequences associated to chemoautotrophic sulphur-oxidizing Epsilon- and Gammaproteobacteria, whereas ¹³C-bicarbonate biomarker labelling suggested that these sulphur-oxidizing bacteria were active far below the oxygen penetration. A targeted manipulation experiment demonstrated that chemoautotrophic carbon fixation was tightly linked to the heterotrophic activity of the cable bacteria down to cm depth. Overall, the results suggest that electrogenic sulphur oxidation is performed by a microbial consortium, consisting of chemoorganotrophic cable bacteria and chemolithoautotrophic Epsilon- and Gammaproteobacteria. The metabolic linkage between these two groups is presently unknown and needs further study.

Prevalence and antimicrobial resistance of Arcobacter species isolated from poultry meat in Iran

1. The objective of this study was to determine the prevalence and antimicrobial resistance of Arcobacter spp. isolated from different species of retail poultry meat in Iran. 2. From August 2012 to April 2013, a total of 540 raw poultry meat samples from chicken (n = 100), turkey (n = 100), quail (n = 100), partridge (n = 80), duck (n = 50), ostrich (n = 60) and geese (n = 50) were purchased from randomly selected retail outlets in Shahrekord, Isfahan, Sari and Rasht, Iran. 3. Using culture techniques, 71 of 540 poultry meat samples (13.1%) were positive for Arcobacter spp. The highest prevalence of Arcobacter spp. was found in chicken meat (28.0%), followed by quail (12.0%), duck (11.4%), turkey (11.0%), geese (8.0%), partridge (7.5%) and ostrich (3.3%) meat. The number of A. butzleri isolated from poultry meat samples (90.1%) was significantly higher than A. cryaerophilus (7.1%) and A. skirrowii (2.8%). Significantly more poultry meat samples were found to contain Arcobacter spp. by the PCR assay than by the culture method. 4. Susceptibilities of Arcobacter isolates were determined for 14 antimicrobial drugs using the disk diffusion method. All of the 71 Arcobacter isolates tested were resistant to one or more antimicrobial agents. Resistance to cephalothin and vancomycin (95.8%) was the most common finding, followed by resistance to methicillin, azithromycin and ampicillin. All Arcobacter isolates were susceptible to gentamicin, streptomycin, tetracyclin and kanamycin. 5. The results of this study indicated the importance of poultry meat, especially chicken meat, as potential sources of Arcobacter spp. infection in people. Furthermore, the strains indicated resistance to a broad spectrum of antibiotics.

Arcobacter ebronensis sp. nov. and Arcobacter aquimarinus sp. nov., two new species isolated from marine environment

Two strains recovered from mussels (F128-2(T)) and sea water (W63(T)) were characterized as Arcobacter sp., but they could not be assigned to any known species using the molecular identification methods specific for this genus (16S rDNA-RFLP and m-PCR) and rpoB gene analysis. The 16S rRNA gene sequence similarity to the type strains of all Arcobacter species ranged from 92.2% to 96.7% with strain F128-2(T), and from 94.1% to 99.4% with strain W63(T), the most similar being A. bivalviorum (CECT 7835(T)) and A. defluvii (CECT 7697(T)), respectively. The phylogenetic analyses of 16S rRNA, and the concatenated sequences of gyrB, gyrA, rpoB, atpA and hsp60 genes confirmed that strains F128-2(T) and W63(T) belonged to two new lineages within the genus Arcobacter. Moreover, both strains showed differential phenotypic characteristics and MALDI-TOF mass spectra from all other Arcobacter species. Therefore, it has been demonstrated the existence of two new Arcobacter species and the proposed names are Arcobacter ebronensis (type strain F128-2(T)=CECT 8441(T)=LMG 27922(T)), and Arcobacter aquimarinus (type strain W63(T)=CECT 8442(T)=LMG 27923(T)).

Snow surface microbiome on the High Antarctic Plateau (DOME C)

The cryosphere is an integral part of the global climate system and one of the major habitable ecosystems of Earth's biosphere. These permanently frozen environments harbor diverse, viable and metabolically active microbial populations that represent almost all the major phylogenetic groups. In this study, we investigated the microbial diversity in the surface snow surrounding the Concordia Research Station on the High Antarctic Plateau through a polyphasic approach, including direct prokaryotic quantification by flow cytometry and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), and phylogenetic identification by 16S RNA gene clone library sequencing and 454 16S amplicon pyrosequencing. Although the microbial abundance was low (<10³ cells/ml of snowmelt), concordant results were obtained with the different techniques. The microbial community was mainly composed of members of the Alpha-proteobacteria class (e.g. Kiloniellaceae and Rhodobacteraceae), which is one of the most well-represented bacterial groups in marine habitats, Bacteroidetes (e.g. Cryomorphaceae and Flavobacteriaceae) and Cyanobacteria. Based on our results, polar microorganisms could not only be considered as deposited airborne particles, but as an active component of the snowpack ecology of the High Antarctic Plateau.

Prevalence and antimicrobial susceptibility of Arcobacter species in cow milk, water buffalo milk and fresh village cheese

In this study, the presence of Arcobacter spp. was examined in cow milk (n=50), water buffalo (WB) milk (n=50) and fresh village cheese (n=50) samples. The 16S rDNA-RFLP method was used for the identification of Arcobacter spp. The disc diffusion method was used to investigate the susceptibility of all strains identified to 18 different antimicrobial substances. The most commonly isolated Arcobacter species were found to be Arcobacter butzleri (38.89%), Arcobacter cryaerophilus (22.23%) and Arcobacter skirrowii (11.12%) in cow milk; A. cryaerophilus (33.33%), Arcobacter cibarius (20.83%) and A. butzleri (12.50%) in WB milk; and A. skirrowii (28.57%), A. butzleri (21.43%) and A. cryaerophilus (14.29%) in fresh village cheese. This is the first study to identify the presence of Arcobacter nitrofigilis, Arcobacter cloacae, Arcobacter halophilus, Arcobacter bivalviorum and A. cibarius species in analyzed samples. It was found that all of the A. cryaerophilus (n:16) isolates were resistant to cefoperazone, cloxacillin and penicillin G; all of the A. skirrowii (n:12) and A. butzleri (n:10) isolates were resistant to cefoperazone, tetracycline, ampicillin, erythromycin, cloxacillin and penicillin G. It was concluded that cow milk, WB milk and fresh village cheese samples are an important source of Arcobacter species and pose a risk to public health.

Genus-specific PCR assay for screening Arcobacter spp. in chicken meat

BACKGROUND

The number of emerging pathogenic species described within the genus Arcobacter has increased rapidly during the last few years. In this work a genus-specific polymerase chain reaction (PCR) assay was developed for detection of the species of Arcobacter most commonly associated with foods. The assay uses primers designed to amplify an 85 bp DNA fragment on the 16S rRNA gene and was applied to the detection of Arcobacter spp. in retail chicken meat.

RESULTS

Primer specificity was tested against a panel of Arcobacter spp., related Campylobacter and Helicobacter spp. and other food bacteria. Arcobacter primers consistently and selectively amplified the expected DNA fragment in all tested Arcobacter spp. Bacterial control primers confirmed the presence of amplifiable DNA in the samples. The applicability of the PCR assay to food was validated through screening of fresh retail chicken samples for the presence of Arcobacter spp., with a result of 45% (23 out of 51) positive samples.

CONCLUSION

The genus-specific PCR assay developed has the potential to be used as a quick and sensitive alternative method for the survey of Arcobacter contamination in meats.

Comparison of conventional PCR, multiplex PCR, and loop-mediated isothermal amplification assays for rapid detection of Arcobacter species

This study aimed to develop a loop-mediated isothermal amplification (LAMP) method for the rapid detection of Arcobacter species. Specific primers targeting the 23S ribosomal RNA gene were used to detect Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii. The specificity of the LAMP primer set was assessed using DNA samples from a panel of Arcobacter and Campylobacter species, and the sensitivity was determined using serial dilutions of Arcobacter species cultures. LAMP showed a 10- to 1,000-fold-higher sensitivity than multiplex PCR, with a detection limit of 2 to 20 CFU per reaction in vitro. Whereas multiplex PCR showed cross-reactivity with Campylobacter species, the LAMP method developed in this study was more sensitive and reliable than conventional PCR or multiplex PCR for the detection of Arcobacter species.

Arcobacter anaerophilus sp. nov., isolated from an estuarine sediment and emended description of the genus Arcobacter

Two strains (JC83, JC84T) of obligately anaerobic, H2S-producing bacteria were isolated from estuarine sediment samples collected from Gangasagar, West Bengal, India. Cells were Gram-stain-negative, non-motile rods. Both strains were positive for oxidase, negative for catalase, hydrolysed casein, reduced nitrate and utilized citrate. Both strains grew chemoorganoheterotrophically with optimal pH of 7–8 (range 7–10) and at 30 °C (range 25–37 °C). C16 : 1ω7c, C18 : 1ω7c, C16 : 0 and C12 : 0 were the major fatty acids of both strains with minor amounts of C14 : 0, C12 : 0 3-OH and C18 : 0. Polar lipids of both strains included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, phosphatidylcholine, phosphatidylinositol, an unidentified aminolipid (AL2), an unidentified phospholipid (PL2) and an unidentified lipid (L3). MK-6 was the major respiratory quinone. The DNA G+C content of strains JC83 and JC84T was 25.0 and 24.6 mol%, respectively. The strains showed DNA reassociation >85 % (86.0±0.5 %) (based on DNA–DNA hybridization). Based on 16S rRNA gene sequence analysis, both strains were identified as belonging to the family Campylobacteraceae of the class Epsilonproteobacteria with Arcobacter marinus CL-S1T (95.4 % sequence similarity) as their closest phylogenetic neighbour. On the basis of morphological, physiological and chemotaxonomic characteristics as well as phylogenetic analysis, strains JC83 and JC84T are considered to represent a novel species, for which the name Arcobacter anaerophilus sp. nov. is proposed. The type strain is JC84T ( = KCTC 15071T = MTCC 10956T = DSM 24636T). An emended description of the genus Arcobacter is provided.

Archaeal and bacterial diversity in an arsenic-rich shallow-sea hydrothermal system undergoing phase separation

Phase separation is a ubiquitous process in seafloor hydrothermal vents, creating a large range of salinities. Toxic elements (e.g., arsenic) partition into the vapor phase, and thus can be enriched in both high and low salinity fluids. However, investigations of microbial diversity at sites associated with phase separation are rare. We evaluated prokaryotic diversity in arsenic-rich shallow-sea vents off Milos Island (Greece) by comparative analysis of 16S rRNA clone sequences from two vent sites with similar pH and temperature but marked differences in salinity. Clone sequences were also obtained for aioA-like functional genes (AFGs). Bacteria in the surface sediments (0–1.5 cm) at the high salinity site consisted of mainly Epsilonproteobacteria (Arcobacter sp.), which transitioned to almost exclusively Firmicutes (Bacillus sp.) at ~10 cm depth. However, the low salinity site consisted of Bacteroidetes (Flavobacteria) in the surface and Epsilonproteobacteria (Arcobacter sp.) at ~10 cm depth. Archaea in the high salinity surface sediments were dominated by the orders Archaeoglobales and Thermococcales, transitioning to Thermoproteales and Desulfurococcales (Staphylothermus sp.) in the deeper sediments. In contrast, the low salinity site was dominated by Thermoplasmatales in the surface and Thermoproteales at depth. Similarities in gas and redox chemistry suggest that salinity and/or arsenic concentrations may select for microbial communities that can tolerate these parameters. Many of the archaeal 16S rRNA sequences contained inserts, possibly introns, including members of the Euryarchaeota. Clones containing AFGs affiliated with either Alpha- or Betaproteobacteria, although most were only distantly related to published representatives. Most clones (89%) originated from the deeper layer of the low salinity, highest arsenic site. This is the only sample with overlap in 16S rRNA data, suggesting arsenotrophy as an important metabolism in similar environments.

Adherence to and invasion of human intestinal cells by Arcobacter species and their virulence genotypes

The genus Arcobacter is composed of 17 species which have been isolated from various sources. Of particular interest are A. butzleri, A. cryaerophilus, and A. skirrowii, as these have been associated with human cases of diarrhea, the probable transmission routes being through the ingestion of contaminated drinking water and food. To date, only limited studies of virulence traits in this genus have been undertaken. The present study used 60 Arcobacter strains isolated from different sources, representing 16 of the 17 species of the genus, to investigate their ability to adhere to and invade the human intestinal cell line Caco-2. In addition, the presence of five putative virulence genes (ciaB, cadF, cj1349, hecA, and irgA) was screened for in these strains by PCR. All Arcobacter species except A. bivalviorum and Arcobacter sp. strain W63 adhered to Caco-2 cells, and most species (10/16) were invasive. The most invasive species were A. skirrowii, A. cryaerophilus, A. butzleri, and A. defluvii. All invasive strains were positive for ciaB (encoding a putative invasion protein). Other putative virulence genes were present in other species, i.e., A. butzleri (cadF, cj1349, irgA, and hecA), A. trophiarum (cj1349), A. ellisii (cj1349), and A. defluvii (irgA). No virulence genes were detected in strains which showed little or no invasion of Caco-2 cells. These results indicate that many Arcobacter species are potential pathogens of humans and animals.

Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores

We investigated the terminal electron-accepting pathways and the acetate-oxidizing bacteria in surface sediment (0-5 mm depth) of Aarhus Bay, Denmark, in anoxic slurry and intact core incubations. In the intact cores, oxygen, nitrate, oxides of manganese and iron, and sulfate were all available and likely all used as electron acceptors by the microbial community, whereas microbial iron and sulfate reduction dominated in the slurries. The availability of electron acceptors clearly affected which organisms were labeled by 16S rRNA-stable isotope probing (SIP). Members of the Oceanospirillaceae were identified as (13) C-acetate oxidizers in both types of incubations, but bacteria related to Colwellia and Arcobacter oxidized acetate in the intact core, while members of the Desulfuromonadales and Acidithiobacillaceae did so in the slurry incubation. Desulfuromonadales sequences also dominated 16S rRNA gene clone libraries from the highest positive dilution of the acetate-oxidizing most probable number cultures with manganese and iron oxides. Thus, members of Desulfuromonadales are likely important for acetate oxidation coupled to iron and manganese reduction in situ, while the identified Gammaproteobacteria and affiliates of Arcobacter may utilize oxygen, nitrate and manganese oxides. Our study further highlights some of the biases that are associated with the use of RNA-SIP as well as slurry and intact core incubations.

Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile

Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H(2), H(2)S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.

Microbial diversity under extreme euxinia: Mahoney Lake, Canada

Mahoney Lake, British Columbia, Canada, is a stratified, 15-m deep saline lake with a euxinic (anoxic, sulfidic) hypolimnion. A dense plate of phototrophic purple sulfur bacteria is found at the chemocline, but to date the rest of the Mahoney Lake microbial ecosystem has been underexamined. In particular, the microbial community that resides in the aphotic hypolimnion and/or in the lake sediments is unknown, and it is unclear whether the sulfate reducers that supply sulfide for phototrophy live only within, or also below, the plate. Here we profiled distributions of 16S rRNA genes using gene clone libraries and PhyloChip microarrays. Both approaches suggest that microbial diversity is greatest in the hypolimnion (8 m) and sediments. Diversity is lowest in the photosynthetic plate (7 m). Shallower depths (5 m, 7 m) are rich in Actinobacteria, Alphaproteobacteria, and Gammaproteobacteria, while deeper depths (8 m, sediments) are rich in Crenarchaeota, Natronoanaerobium, and Verrucomicrobia. The heterogeneous distribution of Deltaproteobacteria and Epsilonproteobacteria between 7 and 8 m is consistent with metabolisms involving sulfur intermediates in the chemocline, but complete sulfate reduction in the hypolimnion. Overall, the results are consistent with the presence of distinct microbial niches and suggest zonation of sulfur cycle processes in this stratified system.