Successful Treatment of Recurrent Clostridioides difficile Infection Using a Novel, Drinkable, Oral Formulation of Fecal Microbiota.

BACKGROUND: Fecal microbiota transplants can be administered orally in encapsulated form or require invasive procedures to administer liquid formulations. There is a need for an oral liquid formulation of fecal microbiota for patients who are unable to swallow capsules, especially if they require multiple, repeated administrations. AIMS: These studies were conducted to develop a protocol to manufacture an organoleptically acceptable powdered fecal microbiota formulation that can be suspended in a liquid carrier and used for fecal microbiota transplantation. METHODS: Several processing steps were investigated, including extra washes of microbiota prior to lyophilization and an addition of a flavoring agent. The viability of bacteria in the transplant formulation was tested using live/dead microscopy staining and engraftment into antibiotic-treated mice. After development of a clinical protocol for suspension of the powdered microbiota, the new formulation was tested in three elderly patients with recurrent Clostridioides difficile infections and who have difficulties in swallowing capsules. Changes in the microbial community structure in one of the patients were characterized using 16S rRNA gene profiling and engraftment analysis. RESULTS: The processing steps used to produce an organoleptically acceptable suspension of powdered fecal microbiota did not result in loss of its viability. The powder could be easily suspended in a liquid carrier. The use of the new formulation was associated with abrogation of the cycle of C. difficile infection recurrences in the three patients. CONCLUSION: We developed a novel organoleptically acceptable liquid formulation of fecal microbiota that is suitable for use in clinical trials for patients with difficulties in swallowing capsules.

p-Cresol Sulfate Is a Sensitive Urinary Marker of Fecal Microbiota Transplantation and Antibiotics Treatments in Human Patients and Mouse Models.

Fecal microbiota transplantation (FMT) has emerged as a highly effective therapy for recurrent Clostridioides difficile infection (rCDI) and also a potential therapy for other diseases associated with dysbiotic gut microbiota. Monitoring metabolic changes in biofluids and excreta is a noninvasive approach to identify the biomarkers of microbial recolonization and to understand the metabolic influences of FMT on the host. In this study, the pre-FMT and post FMT urine samples from 11 rCDI patients were compared through metabolomic analyses for FMT-induced metabolic changes. The results showed that p-cresol sulfate in urine, a microbial metabolite of tyrosine, was rapidly elevated by FMT and much more responsive than other microbial metabolites of aromatic amino acids (AAAs). Because patients were treated with vancomycin prior to FMT, the influence of vancomycin on the microbial metabolism of AAAs was examined in a mouse feeding trial, in which the decreases in p-cresol sulfate, phenylacetylglycine, and indoxyl sulfate in urine were accompanied with significant increases in their AAA precursors in feces. The inhibitory effects of antibiotics and the recovering effects of FMT on the microbial metabolism of AAAs were further validated in a mouse model of FMT. Overall, urinary p-cresol sulfate may function as a sensitive and convenient therapeutic indicator on the effectiveness of antibiotics and FMT for the desired manipulation of gut microbiota in human patients.

Impacts of biostimulation and bioaugmentation on woodchip bioreactor microbiomes.

Woodchip bioreactors (WBRs) are used to remove nutrients, especially nitrate, from subsurface drainage. The nitrogen removal efficiency of WBRs, however, is limited by low temperatures and the availability of labile carbon. Bioaugmentation and biostimulation are potential approaches to enhance nitrate removal of WBRs under cold conditions, but their effectiveness is still unclear. Here, we clarified the effects of bioaugmentation and biostimulation on the microbiomes and nitrate removal rates of WBRs. As a bioaugmentation treatment, we inoculated WBR-borne cold-adapted denitrifying bacteria Cellulomonas cellasea strain WB94 and Microvirgula aerodenitrificans strain BE2.4 into the WBRs located at Willmar, MN, USA. As a biostimulation treatment, acetate was added to the WBRs to promote denitrification. Woodchip samples were collected from multiple locations in each WBR before and after the treatments and used for the microbiome analysis. The 16S rRNA gene amplicon sequencing showed that the microbiomes changed by the treatments and season. The high-throughput quantitative PCR for nitrogen cycle genes revealed a higher abundance of denitrification genes at locations closer to the WBR inlet, suggesting that denitrifiers are unevenly present in WBRs. In addition, a positive relationship was identified between the abundance of M. aerodenitrificans strain BE2.4 and those of norB and nosZ in the WBRs. Based on generalized linear modeling, the abundance of norB and nosZ was shown to be useful in predicting the nitrate removal rate of WBRs. Taken together, these results suggest that the bioaugmentation and biostimulation treatments can influence denitrifier populations, thereby influencing the nitrate removal of WBRs. IMPORTANCE Nitrate pollution is a serious problem in agricultural areas in the U.S. Midwest and other parts of the world. Woodchip bioreactor is a promising technology that uses microbial denitrification to remove nitrate from agricultural subsurface drainage, although the reactor's nitrate removal performance is limited under cold conditions. This study showed that the inoculation of cold-adapted denitrifiers (i.e., bioaugmentation) and the addition of labile carbon (i.e., biostimulation) can influence the microbial populations and enhance the reactor's performance under cold conditions. This finding will help establish a strategy to mitigate nitrate pollution.

Denitrifying Woodchip Bioreactors: A Microbial Solution for Nitrate in Agricultural Wastewater-A Review.

Nitrate (NO3-) is highly water-soluble and considered to be the main nitrogen pollutants leached from agricultural soils. Its presence in aquatic ecosystems is reported to cause various environmental and public health problems. Bioreactors containing microbes capable of transforming NO3- have been proposed as a means to remediate contaminated waters. Woodchip bioreactors (WBRs) are continuous flow, reactor systems located below or above ground. Below ground systems are comprised of a trench filled with woodchips, or other support matrices. The nitrate present in agricultural drainage wastewater passing through the bioreactor is converted to harmless dinitrogen gas (N2) via the action of several bacteria species. The WBR has been suggested as one of the most cost-effective NO3--removing strategy among several edge-of-field practices, and has been shown to successfully remove NO3- in several field studies. NO3- removal in the WBR primarily occurs via the activity of denitrifying microorganisms via enzymatic reactions sequentially reducing NO3- to N2. While previous woodchip bioreactor studies have focused extensively on its engineering and hydrological aspects, relatively fewer studies have dealt with the microorganisms playing key roles in the technology. This review discusses NO3- pollution cases originating from intensive farming practices and N-cycling microbial metabolisms which is one biological solution to remove NO3- from agricultural wastewater. Moreover, here we review the current knowledge on the physicochemical and operational factors affecting microbial metabolisms resulting in removal of NO3- in WBR, and perspectives to enhance WBR performance in the future.

Structure and Functional Properties of Bacterial Communities in Surface Sediments of the Recently Declared Nutrient-Saturated Lake Villarrica in Southern Chile.

Lake Villarrica, one of Chile's main freshwater water bodies, was recently declared a nutrient-saturated lake due to increased phosphorus (P) and nitrogen (N) levels. Although a decontamination plan based on environmental parameters is being established, it does not consider microbial parameters. Here, we conducted high-throughput DNA sequencing and quantitative polymerase chain reaction (qPCR) analyses to reveal the structure and functional properties of bacterial communities in surface sediments collected from sites with contrasting anthropogenic pressures in Lake Villarrica. Alpha diversity revealed an elevated bacterial richness and diversity in the more anthropogenized sediments. The phylum Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria dominated the community. The principal coordinate analysis (PCoA) and redundancy analysis (RDA) showed significant differences in bacterial communities of sampling sites. Predicted functional analysis showed that N cycling functions (e.g., nitrification and denitrification) were significant. The microbial co-occurrence networks analysis suggested Chitinophagaceae, Caldilineaceae, Planctomycetaceae, and Phycisphaerae families as keystone taxa. Bacterial functional genes related to P (phoC, phoD, and phoX) and N (nifH and nosZ) cycling were detected in all samples by qPCR. In addition, an RDA related to N and P cycling revealed that physicochemical properties and functional genes were positively correlated with several nitrite-oxidizing, ammonia-oxidizing, and N-fixing bacterial genera. Finally, denitrifying gene (nosZ) was the most significant factor influencing the topological characteristics of co-occurrence networks and bacterial interactions. Our results represent one of a few approaches to elucidate the structure and role of bacterial communities in Chilean lake sediments, which might be helpful in conservation and decontamination plans.

Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid region.

Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation-induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co-occurrence pattern, and functionalities along vertical profile (0-500 cm depth) in a semiarid region of China's Loess Plateau. We showed that the effects of afforestation with a deep-rooted legume tree on cropland were greater in deep than that of in top layers, resulting in decreased bacterial beta diversity, more responsive bacterial taxa and functional groups, increased homogeneous selection, and decreased network robustness in deep soils (120-500 cm). Organic carbon and nitrogen decomposition rates and multifunctionality also significantly decreased by afforestation, and microbial carbon limitation significantly increased in deep soils. Moreover, changes in microbial community and functionality in deep layer was largely related to changes in soil moisture. Such negative impacts on deep soils should be fully considered for assessing afforestation's eco-environment effects and for the sustainability of ecosystems because deep soils have important influence on forest ecosystems in semiarid and arid climates.

Differential hydrogen sulfide production by a human cohort in response to animal- and plant-based diet interventions.

BACKGROUND: Hydrogen sulfide (H2S) is a toxic end-product of microbial fermentation produced in the colon that may play a role in the pathogenesis of several diseases, including ulcerative colitis and colon cancer. However, the effect of diet interventions on intestinal burden of H2S gas exposure remains poorly understood. OBJECTIVE: Determine the effect of short-term (1-week) plant- and animal-based eating patterns on ex vivo fecal H2S production in healthy human volunteers. METHODS: The study design was an open-label, cross-over diet study and diets were self-administered. Each participant consumed two interventional diets: 1) an animal-based, low fiber (i.e. western) diet and 2) a plant-based, high fiber diet, separated by a two-week washout period. Participants collected full stool samples at the end of each week, which were processed within 2 h of collection to capture H2S production. Microfluidic qPCR (MFQPCR) was used to simultaneously quantify multiple taxonomic and functional groups involved in sulfate reduction and the fecal microbiota was characterized through high-throughput DNA sequencing. RESULTS: Median H2S production was higher following the animal-based diet compared to the plant-based diet (p = 0.02; median difference 29 ppm/g, 95% CI 16-97). However, there was substantial individual variability and 2 of 11 individuals (18%) produced more H2S on the plant-based diet. Using the top and bottom quartiles of H2S percent change between animal- and plant-based diet weeks to define responders and non-responders, significant taxonomic differences were observed between the responder and non-responder cohorts. CONCLUSIONS: Here we report that substrate changes associated with a 1-week plant-based diet intervention resulted in lower ex vivo H2S production compared to a 1-week animal-based diet intervention in most healthy individuals. However, H2S responsiveness to diet was not uniform across the entire cohort, and potential H2S production enterotypes were characterized that may predict individualized H2S responsiveness to diet.

Halophytes increase rhizosphere microbial diversity, network complexity and function in inland saline ecosystem.

Salinization is an important global environmental problem influencing sustainable development of terrestrial ecosystems. Salt-tolerant halophytes are often used as a promising approach to remedy the saline soils. Yet, how rhizosphere microbes' association and functions vary with halophytes in saline ecosystems remains unclear, restricting our ability to assess the role of halophytes in remedying saline ecosystems. Herein, we examined bacterial and fungal diversities, compositions, and co-occurrence networks in the rhizospheres of six halophytes and bulk soils in a semiarid inland saline ecosystem, and related these parameters to microbial functions. The microbiomes were more diverse and complex and microbial activity and residues were higher in rhizospheres than bulk soils. The connections of taxa in the rhizosphere microbial communities increased with fungi-fungi and bacteria-fungi connections and fungal diversity. The proportion of the fungi-related central connections were larger in rhizospheres (13-73%) than bulk soils (3%). Moreover, microbial activity and residues were significantly correlated with microbial composition and co-occurrence network complexity. These results indicated that enhanced association between fungi and bacteria increased microbial co-occurring network complexity in halophytes rhizosphere, which contributed to the higher microbial functions (microbial activities and residue) in this inland saline ecosystem.

Climate Change Impacts on Microbiota in Beach Sand and Water: Looking Ahead.

Beach sand and water have both shown relevance for human health and their microbiology have been the subjects of study for decades. Recently, the World Health Organization recommended that recreational beach sands be added to the matrices monitored for enterococci and Fungi. Global climate change is affecting beach microbial contamination, via changes to conditions like water temperature, sea level, precipitation, and waves. In addition, the world is changing, and humans travel and relocate, often carrying endemic allochthonous microbiota. Coastal areas are amongst the most frequent relocation choices, especially in regions where desertification is taking place. A warmer future will likely require looking beyond the use of traditional water quality indicators to protect human health, in order to guarantee that waterways are safe to use for bathing and recreation. Finally, since sand is a complex matrix, an alternative set of microbial standards is necessary to guarantee that the health of beach users is protected from both sand and water contaminants. We need to plan for the future safer use of beaches by adapting regulations to a climate-changing world.

Probable role of Cutibacterium acnes in the gut of the polychaete Capitella teleta.

Capitella teleta, a marine polychaete that feeds on a refractory diet consisting of sediment, was shown to contain unique gut microbiota comprised of microbial functional groups involved in fermentation. Results of our previous studies showed that C. teleta's core gut microbiota were dominated by propionibacteria, and that these bacteria were more abundant in worms than in sediment and feces. In order to test the hypothesis that the worm nutritionally benefits from its gut microbiota, we identified, and genetically and biochemically characterized Cutibacterium acnes strains (formerly Propionibacterium acnes) that were isolated from the gut of C. teleta. Here we show that 13 worm-isolated Cutibacterium acnes strains primarily belonged to phylotype group IB, likely as a clonal population. We also provide evidence that all tested strains produced propionate and vitamin B12, which are essential host-requiring microbial metabolites. The presence of C. acnes in C. teleta was not unique to our worm culture and was also found in those obtained from geographically distant laboratories located in the U.S. and Europe. Moreover, populations of worm gut-associated C. acnes increased following antibiotic treatment. Collectively, results of this study demonstrated that C. acnes is a member of the worm's core functional microbiota and is likely selectively favored by the physiology and chemistry of the host gut environment. To our knowledge, this is the first report of the presence of C. acnes in the C. teleta gut. Our data strongly suggest that C. acnes, a bacterium previously studied as an opportunistic pathogen, can likely act as a symbiont in C. teleta providing the host essential nutrients for survival, growth, and reproduction.

Bioaugmentation with As-transforming bacteria improves arsenic availability and uptake by the hyperaccumulator plant Pteris vittata (L).

Inorganic arsenic (As) is a toxic and carcinogenic pollutant that has long-term impacts on environmental quality and human health. Pteris vittata plants hyperaccumulate As from soils. Soil bacteria are critical for As-uptake by P. vittata. We examined the use of taxonomically diverse soil bacteria to modulate As speciation in soil and their effect on As-uptake by P. vittata. Aqueous media inoculated with Pseudomonas putida MK800041, P. monteilii MK344656, P. plecoglossicida MK345459, Ochrobactrum intermedium MK346993 or Agrobacterium tumefaciens MK346997 resulted in the oxidation of 5-30% As(III) and a 49-79% reduction of As(V). Soil inoculated with P. monteilii increased extractable As(III) and As(V) from 0.5 and 0.09 in controls to 0.9 and 0.39 mg As kg-1 soil dry weight, respectively. Moreover, and P. vittata plants inoculated with P. monteilii, P. plecoglossicida, O. intermedium strains, and A. tumefaciens strains MK344655, MK346994, MK346997, significantly increased As-uptake by 43, 32, 12, 18, 16, and 14%, respectively, compared to controls. The greatest As-accumulation (1.9 ± 0.04 g kg-1 frond Dwt) and bioconcentration factor (16.3 ± 0.35) was achieved in plants inoculated with P. monteilii. Our findings indicate that the tested bacterial strains can increase As-availability in soils, thus enhancing As-accumulation by P. vittata. Novelty statement Pteris vittata, a well-known As-hyperaccumulator, has the remarkable ability to accumulate higher levels of As in their above-ground biomass. The As-tolerant bacteria-plant interactions play a significant role in bioremediation by mediating As-redox and controlling As-availability and uptake by P. vittata. Our studies indicated that most of the tested bacterial strains isolated from As-impacted soil significantly enhanced As-uptake by P. vittata. P. monteilii oxidized 20% of As(III) and reduced 50% of As(V), increased As-extraction from soils, and increased As-uptake by 43% greater compared with control. Therefore, these strains associated with P. vittata can be used in large-scale field applications to remediate As-contaminated soil.

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance.

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases.

Corrigendum: Gut Microbiota Associated With Different Sea Lamprey (Petromyzon marinus) Life Stages.

[This corrects the article DOI: 10.3389/fmicb.2021.706683.].

Gut Microbiota Associated With Different Sea Lamprey (Petromyzon marinus) Life Stages.

Sea lamprey (SL; Petromyzon marinus), one of the oldest living vertebrates, have a complex metamorphic life cycle. Following hatching, SL transition into a microphagous, sediment burrowing larval stage, and after 2-10+ years, the larvae undergo a dramatic metamorphosis, transforming into parasitic juveniles that feed on blood and bodily fluids of fishes; adult lamprey cease feeding, spawn, and die. Since gut microbiota are critical for the overall health of all animals, we examined the microbiota associated with SLs in each life history stage. We show that there were significant differences in the gut bacterial communities associated with the larval, parasitic juvenile, and adult life stages. The transition from larval to the parasitic juvenile stage was marked with a significant shift in bacterial community structure and reduction in alpha diversity. The most abundant SL-associated phyla were Proteobacteria, Fusobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Firmicutes, with their relative abundances varying among the stages. Moreover, while larval SL were enriched with unclassified Fusobacteriaceae, unclassified Verrucomicrobiales and Cetobacterium, members of the genera with fastidious nutritional requirements, such as Streptococcus, Haemophilus, Cutibacterium, Veillonella, and Massilia, were three to four orders of magnitude greater in juveniles than in larvae. In contrast, adult SLs were enriched with Aeromonas, Iodobacter, Shewanella, and Flavobacterium. Collectively, our findings show that bacterial communities in the SL gut are dramatically different among its life stages. Understanding how these communities change over time within and among SL life stages may shed more light on the role that these gut microbes play in host growth and fitness.

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change.

Crop migration caused by climatic events has favored the emergence of new soilborne diseases, resulting in the colonization of new niches (emerging infectious diseases, EIDs). Soilborne pathogens are extremely persistent in the environment. This is in large part due to their ability to reside in the soil for a long time, even without a host plant, using survival several strategies. In this regard, disease-suppressive soils, characterized by a low disease incidence due to the presence of antagonist microorganisms, can be an excellent opportunity for the study mechanisms of soil-induced immunity, which can be applied in the development of a new generation of bioinoculants. Therefore, here we review the main effects of climate change on crops and pathogens, as well as the potential use of soil-suppressive microbiota as a natural source of biocontrol agents. Based on results of previous studies, we also propose a strategy for the optimization of microbiota assemblages, selected using a host-mediated approach. This process involves an increase in and prevalence of specific taxa during the transition from a conducive to a suppressive soil. This strategy could be used as a model to engineer microbiota assemblages for pathogen suppression, as well as for the reduction of abiotic stresses created due to global climate change.

A Combined Digital PCR and Next Generation DNA-Sequencing Based Approach for Tracking Nearshore Pollutant Dynamics Along the Southwest United States/Mexico Border.

Ocean currents, multiple fecal bacteria input sources, and jurisdictional boundaries can complicate pollution source tracking and associated mitigation and management efforts within the nearshore coastal environment. In this study, multiple microbial source tracking tools were employed to characterize the impact and reach of an ocean wastewater treatment facility discharge in Mexico northward along the coast and across the Southwest United States- Mexico Border. Water samples were evaluated for fecal indicator bacteria (FIB), Enterococcus by culture-based methods, and human-associated genetic marker (HF183) and Enterococcus by droplet digital polymerase chain reaction (ddPCR). In addition, 16S rRNA gene sequence analysis was performed and the SourceTracker algorithm was used to characterize the bacterial community of the wastewater treatment plume and its contribution to beach waters. Sampling dates were chosen based on ocean conditions associated with northern currents. Evidence of a gradient in human fecal pollution that extended north from the wastewater discharge across the United States/Mexico border from the point source was observed using human-associated genetic markers and microbial community analysis. The spatial extent of fecal contamination observed was largely dependent on swell and ocean conditions. These findings demonstrate the utility of a combination of molecular tools for understanding and tracking specific pollutant sources in dynamic coastal water environments.

CRISPR loci-PCR as Tool for Tracking Azospirillum sp. Strain B510.

Azospirillum-based plant and soil inoculants are widely used in agriculture. The inoculated Azospirillum strains are commonly tracked by both culture-dependent and culture-independent methods, which are time-consuming or expensive. In this context, clustered regularly interspaced short palindromic repeats (CRISPR) loci structure is unique in the bacterial genome, including some Azospirillum species. Here, we investigated the use of CRISPR loci to track specific Azospirillum strains in soils systems by PCR. Primer sets for Azospirillum sp. strain B510 were designed and evaluated by colony and endpoint PCR. The CRISPRloci-PCR approach was standardized for Azospirillum sp. strain B510, and its specificity was observed by testing against 9 different Azospirillum strains, and 38 strains of diverse bacterial genera isolated from wheat plants. The CRISPRloci-PCR approach was validated in assays with substrate and wheat seedlings. Azospirillum sp. strain B510 was detected after of two weeks of inoculation in both sterile and nonsterile substrates as well as rhizosphere grown in sterile substrate. The CRISPRloci-PCR approach was found to be a useful molecular tool for specific tracking of Azospirillum at the strain level. This technique can be easily adapted to other microbial inoculants carrying CRISPR loci and can be used to complement other microbiological techniques.

Rhizobacteria from 'flowering desert' events contribute to the mitigation of water scarcity stress during tomato seedling germination and growth.

Tomato (Solanum lycopersicum L.) is an important vegetable cultivated around the world. Under field conditions, tomato can be negatively affected by water scarcity in arid and semiarid regions. The application of native plant growth-promoting rhizobacteria (PGPR) isolated from arid environments has been proposed as an inoculant to mitigate abiotic stresses in plants. In this study, we evaluated rhizobacteria from Cistanthe longiscapa (syn Calandrinia litoralis and Calandrinia longiscapa), a representative native plant of flowering desert (FD) events (Atacama Desert, Chile), to determine their ability to reduce water scarcity stress on tomato seedlings. The isolated bacterial strains were characterized with respect to their PGPR traits, including P solubilization, 1-aminocyclopropane-1-carboxylate deaminase activity, and tryptophan-induced auxin and exopolysaccharide production. Three PGPR consortia were formulated with isolated Bacillus strains and then applied to tomato seeds, and then, the seedlings were exposed to different levels of water limitations. In general, tomato seeds and seedlings inoculated with the PGPR consortia presented significantly (P ≤ 0.05) greater plant growth (48 to 60 cm of height and 171 to 214 g of weight) and recovery rates (88 to 100%) compared with those without inoculation (37 to 51 cm of height; 146 to 197 g of fresh weight; 54 to 92% of recovery) after exposure to a lack of irrigation over different time intervals (24, 72 and 120 h) before transplantation. Our results revealed the effectiveness of the formulated PGPR consortia from FD to improve the performance of inoculated seeds and seedlings subjected to water scarcity; thus, the use of these consortia can represent an alternative approach for farmers facing drought events and water scarcity associated with climate change in semiarid and arid regions worldwide.

A hybrid DNA sequencing approach is needed to properly link genotype to phenotype in multi-drug resistant bacteria.

Antibiotic resistance genes (ARGs) are now viewed as emerging contaminants posing a potential worldwide human health risk. The degree to which ARGs are transferred to other bacteria via mobile genetic elements (MGEs), including insertion sequences (ISs), plasmids, and phages, has a strong association with their likelihood to function as resistance transfer determinants. Consequently, understanding the structure and function of MGEs is paramount to assessing future health risks associated with ARGs in an environment subjected to strong antibiotic pressure. In this study we used whole genome sequencing, done using MinION and HiSeq platforms, to examine antibiotic resistance determinants among four multidrug resistant bacteria isolated from fish farm effluent in Jeju, South Korea. The combined data was used to ascertain the association between ARGs and MGEs. Hybrid assembly using HiSeq and MinION reads revealed the presence of IncFIB(K) and pVPH2 plasmids, whose sizes were verified using pulsed field gel electrophoresis. Twenty four ARGs and 95 MGEs were identified among the 955 coding sequences annotated on these plasmids. More importantly, 22 of 24 ARGs conferring resistance to various antibiotics were found to be located near MGEs, whereas about a half of the ARGs (11 out of 21) were so in chromosomes. Our results also suggest that the total phenotypic resistance exhibited by the isolates was mainly contributed by these putatively mobilizable ARGs. The study gives genomic insights into the origins of putatively mobilizable ARGs in bacteria subjected to selection pressure.

Corrigendum: Signal Disruption Leads to Changes in Bacterial Community Population.

[This corrects the article DOI: 10.3389/fmicb.2019.00611.].