Pseudomonadales Research Articles

Diversity and dynamics of multiple symbionts contribute to early development of broadcast spawning reef-building coral Dipsastraea veroni.

Sexual reproduction and recruitment enhance the genetic diversity and evolution of reef-building corals for population recovery and coral reef conservation under climate change. However, new recruits are vulnerable to physical changes and the mechanisms of symbiosis establishment remain poorly understood. Here, Dipsastraea veroni, a broadcast spawning hermaphrodite reef-building coral, was subjected to settlement and juvenile growth in flow-through in situ seawater at 27.93 ± 0.96°C. Symbiosis of Symbiodiniaceae, bacteria, and/or archaea by horizontal acquisition and/or hypothetical vertical transmission through the mucus with symbionts from the parent appears to be a heritable process of selection and adaptation in D. veroni at the egg, larva, juvenile (5 days post settlement, d p.s. and 32 d p.s.) stages. Symbiodiniaceae was dominated by the genera Cladocopium, Durusdinium, Symbiodinium, with increasing relative abundance of Durusdinium at 5 d p.s. and Symbiodinium at 32 d p.s. Mixed acquisition of the dominant phyla Pseudomonadota, Bacteroidota, Cyanobacteriota, Bacillota, Planctomycetota, and Actinomycetota in egg, larva, and/or juvenile showed a winnowing and regulated bacterial diversity and dynamics, resulting in stage-abundant orders Pseudomonadales and Bacillales in egg and Rhodobacterales, Rhodospirillales, Cyanobacteria, and Cyanobacteriales in larva and/or juvenile. The photoautotrophic Chloroflexales, Cyanobacteriales, and Chlorobiales were abundant in adults. The stable archaeal community contained predominant Crenarchaeota, Halobacterota, Nanoarchaeia Thermoplasmatota, and eight rare phyla, with increased relative abundance of the genera Bathyarchaeota, Candidatus_Nitrosopumilus, Candidatus_Nitrocosmicus, Nitrosarchaeum, Candidatus_Nitrosotenuis, Candidatus_Nitrosopelagicus, Cenarchaeum, Haladaptatus, Halogranum, Halolamina, and Woesearchaeales and GW2011-AR15 in juveniles. All results revealed flexible symbiotic mechanisms in D. veroni during early ontogeny for coral survival and evolution.IMPORTANCEFlexible symbioses of Symbiodiniaceae, bacteria, and archaea appear to be a heritable process of selection and adaptation in Dipsastraea veroni in the field, benefiting early coral development and facilitating coral population recovery and reef conversation.

Skin Microbiota and Pathological Scars: A Bidirectional Two-Sample Mendelian Randomization Study.

Pathological scars (PSs), resulting from abnormal skin repair, chronic inflammation, and fibrosis, affect millions of people. Previous studies have demonstrated that skin microbiota (SM) plays a role in cutaneous inflammation and healing, but the interplay between PSs and SM remains unclear yet. To investigate the causal associations between SM and two specific PSs: hypertrophic scars (HSs) and keloids. A bidirectional two-sample mendelian randomization (MR) analysis using genetic data for SM, HS, and keloids was conducted. The random-effects inverse variance weighted (IVW) method was used as the primary approach, along with multiple MR methods. False discovery rate (FDR) correction was employed to address multiple testing. In forward analysis, the family Moraxellaceae and order Pseudomonadales exhibited the same significant protective effects on keloids (odds ratio [OR]: 0.849, 95% confidence interval [CI]: 0.770-0.935, q2 = 0.03626). The class Betaproteobacteria (OR: 0.938, 95% CI: 0.894-0.985, q1 = 0.01965) and genus Bacteroides (OR: 0.928, 95% CI: 0.884-0.973, q1 = 0.00889) each demonstrated a suggestive protective effect on HSs and keloids, respectively. Some limited evidence suggested that order Actinomycetales contributes to an increased risk of keloids. In reverse analysis, keloids were found to have negative effects on the class Gammaproteobacteria with limited evidence. There was no detectable evidence of horizontal pleiotropy or heterogeneity. This study provided evidence for the causalities between SM and PSs, which laid foundation for furthering clinical practice and research of microorganism-skin interaction.

An investigation of soil and groundwater metagenomes for genes encoding soluble and particulate methane monooxygenase, toluene-4-monoxygenase, propane monooxygenase and phenol hydroxylase.

Soil and groundwater were investigated for the genes encoding soluble and particulate methane monooxygenase/ammonia monooxygenase (sMMO, pMMO/AMO), toluene 4-monooxygenase (T4MO), propane monooxygenase (PMO) and phenol hydroxylase (PH). The objectives were (1) to determine which subunits were present, (2) to examine the diversity of the phylotypes associated with the biomarkers and (3) to identify which metagenome associated genomes (MAGs) contained these subunits. All T4MO and PH subunits were annotated in the groundwater metagenomes, while few were annotated in the soil metagenomes. The majority of the soil metagenomes included only four sMMO subunits. Only two groundwater metagenomes contained five sMMO subunits. Gene counts for the pMMO subunits varied between samples. The majority of the soil metagenomes were annotated for all four PMO subunits, while three out of eight groundwater metagenomes contained all four PMO subunits. A comparison of the blast alignments for the sMMO alpha chain (mmoX) indicated the phylotypes differed between the soil and groundwater metagenomes. For the pMMO/AMO alpha subunit (pmoA/amoA), Nitrosospira was important for the soil metagenomes, while Methylosinus and Methylocystis were dominant for the groundwater metagenomes. The majority of pmoA alignments from both metagenomes were from uncultured bacteria. High quality MAGs were obtained from the groundwater data. Four MAGs (Methylocella and Cypionkella) contained sMMO subunits. Another three MAGs, within the order Pseudomonadales, contained all three pMMO subunits. All PH subunits were detected in seven MAGs (Azonexus, Rhodoferax, Aquabacterium). In those seven, all contained catechol 2,3-dioxagenase, and Aquabacterium also contained catechol 1,2-dioxygenase. T4MO subunits were detected in eight MAGs (Azonexus, Rhodoferax, Siculibacillus) and all, except one, contained all six subunits. Four MAGs (Rhodoferax and Azonexus) contained all subunits for PH and T4MO, as well as catechol 2,3-dixoygenase. The detection of T4MO and PH in groundwater metagenomes and MAGs has important implications for the potential oxidation of groundwater contaminants.

The Causal Relationship Between Skin Microbiota and Facial Aging: A Mendelian Randomization Study.

Facial aging is a complex process influenced by environmental factors, genetics, and lifestyle. The contribution of the skin microbiota to this process remains poorly understood. This two-sample Mendelian randomization (MR) study was performed using genome-wide genotype data from the UK Biobank and previously published studies on skin microbiota. The primary approach for MR analyses included inverse-variance weighting (IVW), MR-Egger regression, simple mode, weighted median, and weighted mode methods. Sensitivity analyses were performed to assess heterogeneity and pleiotropy, and reverse-direction MR analyses were performed to evaluate potential reverse causation. The MR analysis identified ten skin microbiotas with potential causal relationships with facial aging. Protective skin microbiotas included Genus Finegoldia, ASV011 [Staphylococcus (unc.)], ASV008 [Staphylococcus (unc.)], phylum Firmicutes, Family Rhodobacteraceae, and ASV021 [Micrococcus (unc.)], which were negatively associated with facial aging. Conversely, Order Pseudomonadales, Family Moraxellaceae, ASV039 [Acinetobacter (unc.)], and phylum Bacteroidetes were positively associated with facial aging, indicating a risk factor for accelerated aging. Sensitivity analyses confirmed the robustness of these findings, and reverse-direction MR analyses did not suggest any reverse causation. This study identified specific skin microbial that may influence facial aging and offered new insights into the rejuvenation strategies. This journal requires that authors assign a level of evidence to each submission to which Evidence-Based Medicine rankings are applicable. This excludes Review Articles, Book Reviews, and manuscripts that concern Basic Science, Animal Studies, Cadaver Studies, and Experimental Studies. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

Bacterioplankton Community Diversity of a Portuguese Aquifer System (Maciço Calcário Estremenho)

Climate change may increase the vulnerability of aquifers to contamination through extreme precipitation and extended drought periods. Therefore, the understanding of groundwater ecosystem dynamics is crucial, with bacterial assemblages playing a major role in biogeochemical cycles. The present research describes a geospatial study targeting the bacterial community structure of groundwaters from the largest karst aquifer in Portugal (the Maciço Calcário Estremenho), integrating hydrogeochemical and bacterial diversity data. A total of 22 samples were analyzed from a set of 11 geographically sparsely distributed groundwater sources in dry vs. wet seasons. The 16S rRNA gene barcoding data revealed bacterial community variability across samples in space and time. The phylum Proteobacteria was dominant across all samples (from 44 to 92% of total sequence reads), mainly represented by the classes Alphaproteobacteria (orders Sphingomonadales, BD7–3, Rhizobiales and Rhodospirillales), Betaproteobacteria (orders Burkholderiales, Rhodocyclales, Nitrosomonadales), Gammaproteobacteria (orders Pseudomonadales, Xanthomonadales, Alteromonadales, Legionellales) and Deltaproteobacteria (orders Myxococcales, Spirobacillales). Variation in the bacterial community was primarily attributed to parameters such as redox conditions (DO, ORP), Fe, Mn, SO4, PO4, Sr and Cl, but also some minor and trace elements (Al, V, Cr, Cu, Pb). Our results provide novel insights into bacterial diversity in relation to groundwater hydrogeochemistry. The strong dominance of OTUs related to bacterial taxa associated with nitrification/denitrification also highlights a potentially important role of these assemblages on nutrients (nitrogen sources) and groundwater quality dynamics at this karstic aquifer system. Moreover, the integration of bacterial assemblages information is emphasized as central for water quality monitoring programs.

Comparative analysis of reproductive tract microbiomes in modern and slower-growing broiler breeder lines.

The reproductive tract microbiome in hens is of interest because bacteria in the reproductive tract could potentially affect fertilization and egg production, as well as integrate into the forming egg and vertically transmit to progeny. The reproductive tract microbiome of 37-week-old modern commercial Cobb breeding dams was compared with that of dams from a broiler Legacy line which has not undergone selection since 1986. All animals were kept together under the same management protocol from day of hatch to avoid confounders. In regards to reproductive abilities, Cobb dams' eggs weighed more and the magnum section of their reproductive tract was longer. In regards to microbiome composition, it was found that the reproductive tract microbiomes of the two lines had a lot in common but also that the two breeds have unique reproductive tract microbiomes. Specifically, the order Pseudomonadales was higher in the magnum of Legacy dams, while Verrucomicrobiales was lower. In the infundibulum, Lactobacillales were higher in the Legacy dams while Verrucomicrobiales, Bacteroidales, RF32 and YS2 were lower. our results show that breeding programs have modified not only the physiology of the reproductive tract but also the reproductive tract microbiome. Additional research is required to understand the implications of these changes in the reproductive tract microbiome on the chicken host.

Bacterial decontamination of process liquids and paints in E-coating lines by pulsed electric field treatment

Cultivation-based and DNA-based methods for determining the bacterial load and the composition of the bacterial spectrum have been successfully established for media in electrodip painting, and used for the detailed analysis of the contamination situation in an E-coating system of an automobile plant in Germany. Dominating representatives of the genus Microbacterium spp., the orders Burkholderiales and Pseudomonadales, the family Cytophagaceae and the genera Corynebacterium spp., Sphingomonas spp., and Stenotrophomonas spp. were used for inactivation experiments. Different pulsed electric field (PEF) parameters were studied for an effective and target-directed inactivation of defined bacterial suspensions containing mixtures of Gram-positive as well as Gram-negative bacteria, but also single species suspensions in adequate liquids. PEF treatment with pulse durations longer than 1.0 µs effectively killed bacteria even in low conductivity media, regardless of whether the pulses were unipolar or bipolar, indicating that the choice of pulse shape does not limit the design of the PEF system. Model calculations showed that for efficient treatment in bypass mode, a high treatment flow rate is required rather than a high inactivation efficiency of the PEF treatment. By using specific treatment parameters, such as bipolar pulses of 50 k Vcm−1 and a treatment energy of 40 J mL−1, a significant reduction in both Gram-negative and Gram-positive bacteria (> 2 log10 reduction) can be achieved while minimizing electrode corrosion and coating degradation. PEF treatment proves to be an effective alternative to the use of biocides in an E-coating system and can help maintain a bacteriostatic environment in the system by operating at different points, in transfer flow or bypass mode, ensuring biocide-free operation.

Changes in the prokaryotic communities occurring along a two-stage anaerobic digestion system treating the organic fraction of solid waste

Two-stage anaerobic digestion is useful for recycling of the organic fraction of municipal solid waste and wastewater; the prokaryotic communities involved in this process were characterized using massive sequencing of 16S rRNA gene amplicons. During the 60-day study the prokaryotic communities were stable in time but were affected by their position in the system. The first stage of solid waste digestion was operated in an anaerobic-hydrolytic leach bead reactor with high organic solids content, the microbial communities were dominated by members of the orders Bacteroidales (62%), Selenomonadales (15%), Lactobacillales (13%), Clostridiales (4%) and Rhodospirillales (1%). At this stage, a vertical stratification acted as a transition zone from aerobic to anaerobic environments modifying significantly the composition and structure of bacterial communities.The second stage occurred in an up-flow anaerobic sludge bed reactor specialized in acidogenesis-methanogenesis, where the leachate of the first stage was co-fed with municipal wastewater. In this stage, the bacterial community was dominated by members of the orders Pseudomonadales, Clostridiales, Burkholderiales, Bacteroidales and Syntrophobacterales (accounting for 52%), while the most abundant orders of the archaeal community corresponded to Methanosarcinales (72%) and Methanobacteriales (13%), both of them with methanogenic capacity.

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts.

In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.

Host range of strand-biased circularizing integrative elements: a new class of mobile DNA elements nesting in Gammaproteobacteria

BackgroundThe strand-biased circularizing integrative elements (SEs) are putatively non-mobilizable integrative elements for transmitting antimicrobial resistance genes. The transposition mode and the prevalence of SEs in prokaryotes remain vague.ResultsTo corroborate the transposition mode and the prevalence of SEs, hypothetical transposition intermediates of an SE were searched for in genomic DNA fractions of an SE host. Then, the SE core genes were defined based on gene knockout experiments, and the synteny blocks of their distant homologs were searched for in the RefSeq complete genome sequence database using PSI-BLAST. A genomic DNA fractionation experiment revealed that SE copies are present in a double-stranded nicked circular form in vivo. Operonic structure of three conserved coding sequences (intA, tfp, intB) and srap located at the left end of SEs were identified as essential for attL × attR recombination. The synteny blocks of tfp and srap homologs were detected in 3.6% of the replicons of Gammaproteobacteria but not in other taxa, implying that SE movement is host-dependent. SEs have been discovered most frequently in the orders Vibrionales (19% of replicons), Pseudomonadales (18%), Alteromonadales (17%), and Aeromonadales (12%). Genomic comparisons revealed 35 new SE members with identifiable termini. SEs are present at 1 to 2 copies per replicon and have a median length of 15.7 kb. Three newly identified SE members carry antimicrobial resistance genes, like tmexCD-toprJ, mcr-9, and blaGMA-1. Further experiments validated that three new SE members possess the strand-biased attL × attR recombination activity.ConclusionsThis study suggested that transposition intermediates of SEs are double-stranded circular DNA. The main hosts of SEs are a subset of free-living Gammaproteobacteria; this represents a rather narrow host range compared to those of mobile DNA element groups discovered to date. As the host range, genetic organization, and movements are unique among the mobile DNA elements, SEs provide a new model system for host-mobile DNA element coevolution studies.

Potential values of formalin-fixed paraffin-embedded tissues for intratumoral microbiome analysis in breast cancer

Breast cancer (BC) tissues have been proved to harbor microorganisms, which could potentially contribute to oncogenesis. Formalin-fixed paraffin-embedded (FFPE) tissues are the most widespread clinical samples in BC research. To verify the potential of FFPE tissues in microbiological analysis, we analyzed the microbial communities of FFPE and fresh frozen (FF) tumor samples from 30 participants diagnosed with BC deploying 16S rRNA sequencing. The operational taxonomic units (OTUs) analysis showed that 78.55% of OTUs in FFPE samples were consistent with FF samples. The composition of core bacteria did not change much, and there is also no difference in alpha diversity between FFPE and FF (without unclassified bacteria). Taxonomic variation results show that Firmicutes and Bacteroidota phyla, and their major classes, maintained the same proportion under two preservation methods. In addition, the major class Gammaproteobacteria, as well as its dominant orders Burkholderiales and Pseudomonadales all showed no significant difference in paired analysis. Moreover, the Proteobacteria and Actinobacteriota phyla showed no significant difference between FFPE and FF samples after subtracting unclassified bacteria. Therefore, premised with the intrinsic tumor heterogeneity and unclassified bacteria, there are potential values of FFPE tissues for intratumoral microbiome analysis in breast cancer.

The Effects of Shaking Duration on the Abundance and the Community of Aerobic Denitrifying Bacteria in Shrimp Pond Water and Sediment Samples

With the rapid development of intensive aquaculture, the considerable release of nitrogenous organic compounds has become a serious threat to aquatic organisms. Currently, isolating autochthonous aerobic denitrifying bacteria (ADB) from aquaculture environments is essential for the biological elimination of nitrogenous pollutants. In this study, the enrichment of ADB from shrimp pond water and sediment samples was conducted under different shaking durations. The absolute abundance of total bacteria, nosZ-type, and the napA-type ADB was measured using qPCR. High-throughput sequencing of 16S rRNA, nosZ, and napA genes was performed to reveal the community structure of bacteria and ADB, respectively. Our data revealed that absolute abundance and the community structure of the total bacteria, nosZ-type and napA-type ADB, were significantly altered under different shaking durations. Specifically, the order Pseudomonadales, possessing both nosZ and napA genes, was significantly enriched in water and sediment samples under both 12/12 and 24/0 shaking/static cycles. However, in water samples, compared to the 24/0 shaking/static cycles, the 12/12 shaking/static cycles could lead to a higher enrichment rate of aerobic denitrification bacteria indicated by the higher absolute abundance of bacteria and the higher accounting percentage of orders Oceanospirillales and Vibrionales. Moreover, although the order Pseudomonadales notably increased under the 12/12 of shake/static cycle compared to the 24/0 shaking/static cycle, considering the relative higher abundance of ADB in 24/0 shaking/static cycle, the enrichment of ADB in sediment may be efficient with the 24/0 shaking/static cycle.

Impact of phosphorus limitation on medium-chain-length polyhydroxyalkanoate production by activated sludge

For a sustainable economy, biodegradable biopolymers polyhydroxyalkanoates (PHA) are desirable substitutes to petroleum-based plastics that contaminate our environment. Medium-chain-length (MCL) PHA bioplastics are particularly interesting due to their thermoplastic properties. To hamper the high cost associated to PHA production, the use of bacterial mixed cultures cultivated in open systems and using cheap resources is a promising strategy. Here, we studied the operating conditions favouring direct MCL accumulation by activated sludge, using oleic acid as a model substrate and phosphorus limitation in fed-batch bioreactors. Our results confirm the presence of PHA-accumulating organisms (PHAAO) in activated sludge able to accumulate MCL from oleic acid. A positive correlation between phosphorus (P) limitation and PHA accumulation was demonstrated, allowing up to 26% PHA/total biomass accumulation, and highlighted its negative impact on the MCL/PHA fraction in the polymer. Diversity analysis through 16S rRNA amplicon sequencing revealed a differential selection of PHAAO according to the P-limitation level. A differential behaviour for the orders Pseudomonadales and Burkholderiales at increasing P-limitation levels was revealed, with a higher abundance of the latter at high levels of P-limitation. The PHA accumulation observed in activated sludge open new perspectives for MCL-PHA production system based on P-limitation strategy applied to mixed microbial communities. KEY POINTS: • Direct accumulation of MCL-PHA in activated sludge was demonstrated. • MCL-PHA content is negatively correlated with P-limitation. • Burkholderiales members discriminate the highest P-limitation levels.

A comparative pilot study on Gram-negative bacteria contaminating the hands of children living in urban and rural areas of Indonesia versus Germany - A suitable monitoring strategy for diarrhea risk assessment?

Diarrhea is the second leading cause of death mainly effecting young children. Often it is the result of fecal-oral pathogen transmission. We aimed to investigate whether monitoring the prevalence of Gram-negative bacteria on the hands of asymptomatic children is suitable as an indicator of fecal contamination of the environment in their playground. We compared the prevalence of Gram-negative bacteria on the hands of children, who live in the German city of Göttingen, an urban area in a high-income country, with the situation in Medan as an urban area and Siberut as a rural area both in the middle-income country Indonesia. A total of 511 children at the age of 3 months to 14 years were asked to put their thumb print on MacConkey agar, which was used to screen for the presence of Gram-negative bacteria. These were subsequently identified by using MALD-TOF mass spectrometry and classified into the order Enterobacterales, Pseudomonadales, and others. The highest burden of hand contamination was found in children from rural Siberut (66.7%) followed by children from urban Medan (53.9%), and from urban Göttingen (40.6%). In all three study sites, hand contamination was lower in the youngest (<1 year) and oldest age groups (10-14 years) and highest in the age group 5-9 years. Bacteria of the order Enterobacterales possibly indicating fecal contamination were most prevalent in Siberut (85.1%) followed by Medan (62.9%) and Göttingen (21.5%). Most facultative and obligate gastrointestinal pathogens such as Escherichia coli (n = 2) and Providencia rettgeri (n = 7), both being members of the order Enterobacterales, as well as Aeromonas caviae (n = 5), and Vibrio cholerae (n = 1) both belonging to other orders were nearly exclusively identified on the hands of children in Siberut. This result was not surprising, because hygienic conditions were lowest in Siberut. Only one isolate of A. caviae was found in Medan, and no facultative gastrointestinal pathogen was identified on the hands of children from Göttingen. Our pilot study therefore indicates that investigating hands of children for the prevalence of Gram-negative bacteria using selective media are a helpful method to monitor hygienic conditions, and thereby assess the risk for diarrhea-causing bacterial pathogens in the environment.

Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species.

Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.

Snow-Dependent Biogeochemical Cycling of Polycyclic Aromatic Hydrocarbons at Coastal Antarctica.

The temporal trend of polycyclic aromatic hydrocarbons (PAHs) in coastal waters with highly dynamic sources and sinks is largely unknown, especially for polar regions. Here, we show the concurrent measurements of 73 individual PAHs and environmental data, including the composition of the bacterial community, during three austral summers at coastal Livingston (2015 and 2018) and Deception (2017) islands (Antarctica). The Livingston 2015 campaign was characterized by a larger snow melting input of PAHs and nutrients. The assessment of PAH diagnostic ratios, such as parent to alkyl-PAHs or LMW to HMW PAHs, showed that there was a larger biodegradation during the Livingston 2015 campaign than in the Deception 2017 and Livingston 2018 campaigns. The biogeochemical cycling, including microbial degradation, was thus yearly dependent on snow-derived inputs of matter, including PAHs, consistent with the microbial community significantly different between the different campaigns. The bivariate correlations between bacterial taxa and PAH concentrations showed that a decrease in PAH concentrations was concurrent with the higher abundance of some bacterial taxa, specifically the order Pseudomonadales in the class Gammaproteobacteria, known facultative hydrocarbonoclastic bacteria previously reported in degradation studies of oil spills. The work shows the potential for elucidation of biogeochemical processes by intensive field-derived time series, even in the harsh and highly variable Antarctic environment.

The lung microbiome, peripheral gene expression, and recurrence-free survival after resection of stage II non-small cell lung cancer

BackgroundCancer recurrence after tumor resection in early-stage non-small cell lung cancer (NSCLC) is common, yet difficult to predict. The lung microbiota and systemic immunity may be important modulators of risk for lung cancer recurrence, yet biomarkers from the lung microbiome and peripheral immune environment are understudied. Such markers may hold promise for prediction as well as improved etiologic understanding of lung cancer recurrence.MethodsIn tumor and distant normal lung samples from 46 stage II NSCLC patients with curative resection (39 tumor samples, 41 normal lung samples), we conducted 16S rRNA gene sequencing. We also measured peripheral blood immune gene expression with nanoString®. We examined associations of lung microbiota and peripheral gene expression with recurrence-free survival (RFS) and disease-free survival (DFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression, and examined predictive accuracy using time-dependent receiver operating characteristic (ROC) curves.ResultsOver a median of 4.8 years of follow-up (range 0.2–12.2 years), 43% of patients experienced a recurrence, and 50% died. In normal lung tissue, a higher abundance of classes Bacteroidia and Clostridia, and orders Bacteroidales and Clostridiales, were associated with worse RFS, while a higher abundance of classes Alphaproteobacteria and Betaproteobacteria, and orders Burkholderiales and Neisseriales, were associated with better RFS. In tumor tissue, a higher abundance of orders Actinomycetales and Pseudomonadales were associated with worse DFS. Among these taxa, normal lung Clostridiales and Bacteroidales were also related to worse survival in a previous small pilot study and an additional independent validation cohort. In peripheral blood, higher expression of genes TAP1, TAPBP, CSF2RB, and IFITM2 were associated with better DFS. Analysis of ROC curves revealed that lung microbiome and peripheral gene expression biomarkers provided significant additional recurrence risk discrimination over standard demographic and clinical covariates, with microbiome biomarkers contributing more to short-term (1-year) prediction and gene biomarkers contributing to longer-term (2–5-year) prediction.ConclusionsWe identified compelling biomarkers in under-explored data types, the lung microbiome, and peripheral blood gene expression, which may improve risk prediction of recurrence in early-stage NSCLC patients. These findings will require validation in a larger cohort.

Time after time: detecting annual patterns in stream bacterial biofilm communities.

SummaryTo quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.

Bacterial Metabolic Potential and Micro-Eukaryotes Enriched in Stony Coral Tissue Loss Disease Lesions

The epizootic disease outbreak known as stony coral tissue loss disease (SCTLD) is arguably the most devastating coral disease in recorded history. SCTLD emerged off the coast of South Florida in 2014 and has since moved into the Caribbean, resulting in coral mortality rates that have changed reef structure and function. Currently, the cause of SCTLD is unknown, but there is evidence from 16S rRNA gene sequencing and bacterial culture studies that the microbial community plays a role in the progression of SCTLD lesions. In this study, we applied shotgun metagenomics to characterize the potential function of bacteria, as well as the composition of the micro-eukaryotic community, associated with SCTLD lesions. We re-examined samples that were previously analyzed using 16S rRNA gene high-throughput sequencing from four coral species: Stephanocoenia intersepta, Diploria labyrinthiformis, Dichocoenia stokesii, and Meandrina meandrites. For each species, tissue from apparently healthy (AH) corals, and unaffected tissue (DU) and lesion tissue (DL) on diseased corals, were collected from sites within the epidemic zone of SCTLD in the Florida Keys. Within the micro-eukaryotic community, the taxa most prominently enriched in DL compared to AH and DU tissue were members of Ciliophora. We also found that DL samples were relatively more abundant in less energy-efficient pathways like the pentose phosphate pathways. While less energy-efficient processes were identified, there were also relatively higher abundances of nucleotide biosynthesis and peptidoglycan maturation pathways in diseased corals compared to AH, which suggests there was more bacteria growth in diseased colonies. In addition, we generated 16 metagenome-assembled genomes (MAGs) belonging to the orders Pseudomonadales, Beggiatoales, Rhodobacterales, Rhizobiales, Rs-D84, Flavobacteriales, and Campylobacterales, and all MAGs were enriched in DL samples compared to AH samples. Across all MAGs there were antibiotic resistance genes that may have implications for the treatment of SCTLD with antibiotics. We also identified genes and pathways linked to virulence, such as nucleotide biosynthesis, succinate dehydrogenase, ureases, nickel/iron transporters, Type-1 secretion system, and metalloproteases. Some of these enzymes/pathways have been previously targeted in the treatment of other bacterial diseases and they may be of interest to mitigate SCTLD lesion progression.

Achieving rapid mainstream deammonification through inoculating long-term refrigerated sidestream sludge in plug-flow fixed-bed biofilm reactor

The start-up of a stable mainstream deammonification requires sufficient anaerobic ammonia-oxidizing bacteria (AnAOB). This study used a plug-flow fixed-bed reactor (PFBR) to verify the feasibility of establishing the mainstream deammonification system by inoculating the sidestream sludge after long-term refrigeration. A rapid resuscitation of the mainstream deammonification system was accomplished by controlling the front-end aeration rate of the PFBR. Results showed that the system was rapidly resuscitated in 44 days eventually with the nitrogen removal rate and nitrogen removal efficiency of 0.1 kg N·(m3·d)−1 and 79.1%, respectively. Also, the efficient performance was secured by the proportionate approaching equilibrium of AnAOB and ammonia-oxidizing bacteria (AOB) activity of 2.35 ± 0.40 and 2.60 ± 0.29 mg N·(g VSS·h)−1, respectively. In addition, Pearson correlation analysis revealed that AnAOB abundance (detected Candidatus Kuenenia) negatively correlated with the AOB (mainly Nitrosomonas)/AnAOB abundance ratio, while correlated positively with the residual ammonium concentration of a region. Furthermore, long-term refrigeration probably reduced the cross-feed relationship between AnAOB and other symbiotic organisms (Armatimonadetes and Chloroflexi) to maintain the basic metabolism. Meanwhile, extracellular polymeric substances produced by other genera (order Xanthomonadales and Pseudomonadales) decreased the mass transfer, protecting AnAOB from unfavorable conditions, thereby facilitating high AnAOB abundance during refrigeration. Thus, this study provides a promising perspective towards the practical applications of mainstream process.