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Bibliography on: Microbial Ecology

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ESP: PubMed Auto Bibliography 24 Sep 2018 at 01:34 Created: 

Microbial Ecology

Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

Created with PubMed® Query: "microbial ecology" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2018-09-23

Shteindel N, Yankelev D, Y Gerchman (2018)

High-Throughput Quantitative Measurement of Bacterial Attachment Kinetics on Seconds Time Scale.

Microbial ecology pii:10.1007/s00248-018-1254-5 [Epub ahead of print].

Surface attachment is an important factor in the life of many microbial species. Late stages of attachment (i.e., mature biofilms) are rigorously studied, but data on the very early stages is scarce. The lack of robust research methods may go a long way in explaining this situation. We have developed a method that allows the rapid kinetic measurement of bacterial attachment, with seconds to minute's temporal resolution, in a high-throughput setting. The method requires the use of a commercially available microtiter plate reader capable of fluorescence measurement from the bottom, standard microtiter plates, fluorescently tagged bacteria, and a common dye. The high temporal resolution reveals nuanced, fast, and dynamic behaviors in the very early phases of attachment. To demonstrate potential applications, we tested the effect of various conditions on attachment kinetics-specie, substratum, salt concentration, and culture density. Results are in good agreement with crystal violet staining (correlation R2 > 0.95 in all cases) and reproducing published data but show much greater detail and fidelity.

RevDate: 2018-09-23

Podduturi R, NOG Jørgensen (2018)

Conidia-based fluorescence quantification of Streptomyces.

Journal of microbiological methods pii:S0167-7012(18)30703-6 [Epub ahead of print].

Determination of cell numbers in filamentous bacteria, such as Streptomyces, is challenging due to the tangled and twisted structure of the filaments and formation of cell clumps in liquid cultures. Here, we developed a conidia-based approach, in which fluorescence of conidia, after staining with the DNA-binding stain SYBR Green 1, was related to SYBR Green 1 fluorescence of DNA in Streptomyces. When cell number in Streptomyces filaments, determined by the conidia assay, was compared to number obtained by a qPCR assay, 34 to 62% of cells in the Streptomyces filaments were recovered. The difference in numbers probably reflects an insufficient extraction of DNA from the Gram-positive bacteria, rather than underestimation of the actual cell number by the conidia-based determination. The conidia-based approach appears to be a fast and reliable procedure for counting cell numbers in Streptomyces filaments but it can also be used for other filamentous bacteria, if proper standard curves can be made.

RevDate: 2018-09-22

Wen D, Chang NB, MP Wanielista (2018)

Comparative copper toxicity impact and enzymatic cascade effect on Biosorption Activated Media and woodchips for nutrient removal in stormwater treatment.

Chemosphere, 213:403-413 pii:S0045-6535(18)31717-X [Epub ahead of print].

Copper, a commonly occurring heavy metal in stormwater runoff, was tested for its inhibitory effects on key nitrogen cycle bacteria in Biosorption Activated Media (BAM) and woodchip. The information in this paper is used to show that copper can enhance the denitrification process through enzyme cascade reactions since nitrous reductase is the enzyme responsible for the last step of denitrification and is largely dependent on copper as its cofactor. However, media characteristics are critical for assessing multi-enzymatic cascade reactions from the microbial ecology point of view. Moreover, both media showed significant copper removal through various mechanisms at 30 cm depth. The bioactivity evaluation indicates that other bacteria (fermentative bacteria, etc.) can be largely depressed with the presence of copper, hence the biofilm structure would be more vulnerable under shearing effects, which may result in holistic depression on the microbial community.

RevDate: 2018-09-22

Mergoni G, Percudani D, Lodi G, et al (2018)

Prevalence of Candida Species in Endodontic Infections: Systematic Review and Meta-analysis.

Journal of endodontics pii:S0099-2399(18)30512-0 [Epub ahead of print].

INTRODUCTION: Candida in endodontic infections has been investigated in a large number of studies, but its role as an endodontic pathogen is still debatable. The aim of this study was to systematically review the literature on the prevalence of Candida species in root canal infections.

METHODS: Extensive literature research was performed in the most important electronic biomedical databases, and additional studies have been identified from references from relevant articles. Studies were critically appraised using a modified version of the Joanna Briggs Institute Critical Appraisal Checklist.

RESULTS: From 2225 unique records, 2118 were excluded on the basis of title and abstract. Of the remaining 107 studies, 50 were excluded after full-text review, and 57 were included for qualitative and quantitative analysis. The overall prevalence of Candida spp. in root canal infections was 8.20% (95% confidence interval, 5.56%-11.21%). Candida albicans was the most frequently isolated species. Significant heterogeneity among studies was observed (P < .001, I2 = 86.07%). Subgroup analyses revealed a higher prevalence of Candida spp. from African samples. All studies considered, a high or unclear risk of bias was prevalent regarding 6 out of the 8 items considered in the critical appraisal.

CONCLUSIONS: Candida spp. occurred in a small proportion of root canal infections. Further and better designed research is needed to investigate the real contribution of Candida spp. to the microbial ecology in infected root canals.

RevDate: 2018-09-21

Florence VH, Kim P, Hugo R, et al (2018)

Mucin Degradation Niche as a Driver of Microbiome Composition and Akkermansia Muciniphila Abundance in a Dynamic Gut Model is Donor Independent.

FEMS microbiology ecology pii:5101425 [Epub ahead of print].

Akkermansia muciniphila, an abundant mucin degrading intestinal bacterium, has been correlated with human health in various studies. The in vitro SHIME model was used to reach a mechanistic understanding of A. muciniphila's colonization preferences and its response to environmental parameters such as colon pH and mucins. These insight can help to identify the optimal conditions for successful in vivo application. After a period of mucin deprivation, we found that mucin supplementation resulted in significantly different microbial communities, with more Akkermansia, Bacteroides and Ruminococcus. Mucin treatment accounted for 26% of the observed variation in the microbial community at OTU level (p=0.001), whereas the donor effect was limited (8%) (p=0.035), indicating mucins to constitute an important ecological niche shaping the microbiota composition. The effect of colonic pH had a less profound impact on the microbiome with both pH and donor origin explaining around 10% of the variability in the dataset. Yet, higher simulated colonic pH had a positive impact on Akkermansia abundance while short chain fatty acid analysis displayed a preference for propionate production with higher colonic pH. Our results show that mucins as nutritional resource are a more important modulator of the gut microbiome than colon pH as environmental factor.

RevDate: 2018-09-21

Roussel C, Galia W, Leriche F, et al (2018)

Comparison of conventional plating, PMA-qPCR, and flow cytometry for the determination of viable enterotoxigenic Escherichia coli along a gastrointestinal in vitro model.

Applied microbiology and biotechnology pii:10.1007/s00253-018-9380-z [Epub ahead of print].

Recent technological advances for bacterial viability assessment using molecular methods or flow cytometry can provide meaningful interest for the demarcation between live and dead microorganisms. Nonetheless, these methods have been scarcely applied to foodborne pathogens and never for directly assessing their viability within the human digestive environment. The purpose of this study was to compare two methods based on membrane integrity (propidium monoazide (PMA) q-PCR and Live/Dead flow cytometry) and the classical plate-count method to determine the viability of a common foodborne pathogen, enterotoxigenic Escherichia coli (ETEC), during its transit trough simulated human gastrointestinal environment. Viable ETEC counts in the gastric and small intestinal compartments of the gastrointestinal TIM model indicated a consensus between the three tested methods (PMA-qPCR, flow cytometry, and plate counts). In a further step, flow cytometry analysis appeared as the preferred method to elucidate ETEC physiological states in the in vitro digestive environment by discriminating four subpopulations, while PMA-qPCR can only distinguish two. The defined viable/altered ETEC population was found during all in vitro digestions, but mainly in the gastric compartment. Being able to discriminate the particular physiological states of pathogenic microorganisms in the digestive environment is of high interest, because if some cells are not observable on culture media, they might keep their ability to express virulence functions.

RevDate: 2018-09-21

Erşan YÇ, Van Tittelboom K, Boon N, et al (2018)

Nitrite producing bacteria inhibit reinforcement bar corrosion in cementitious materials.

Scientific reports, 8(1):14092 pii:10.1038/s41598-018-32463-6.

Chemicals and synthetic coatings are widely used to protect steel against corrosion. Bio-based corrosion inhibition strategies can be an alternative in the arising bioeconomy era. To maintain the good state of steel reinforcement in cracked concrete, microbe-based self-healing cementitious composites (MSCC) have been developed. Yet, proposed strategies involve reasonably slow crack filling by biomineralization and thus risk the possible rebar corrosion during crack healing. Here we upgrade the rebar protection to a higher level by combining MSCC with microbial induced corrosion inhibition. Presented NO3- reducing bacterial granules inhibit rebar corrosion by producing the anodic corrosion inhibitor NO2- and meanwhile heal a 300-µm-wide crack in 28 days. During 120 days exposure to 0.5 M Cl- solution, the rebars in cracked MSCC keep showing open circuit potentials above the critical value of -250 mV and they lose less than 2% of the total rebar material which corresponds to half the material loss in cracked plain mortar. Overall, the obtained rebar protection performance is comparable with that of uncracked mortar and mortar containing chemical inhibitor, hence the microbe-based system becomes an alternative to the traditional methods.

RevDate: 2018-09-21

Fiorentino A, Di Cesare A, Eckert EM, et al (2019)

Impact of industrial wastewater on the dynamics of antibiotic resistance genes in a full-scale urban wastewater treatment plant.

The Science of the total environment, 646:1204-1210.

Urban Wastewater Treatment Plants (UWTPs) treating mixed urban sewage and industrial wastewater are among the major hotspots for the spread of Antibiotic Resistance Genes (ARGs) into the environment. This study addresses the impact of the wastewater origin on ARG dynamics in a full-scale UWTP (15,000 Population Equivalent, PE) by operating the plant with and without industrial wastewater. Composite samples (4 L) from different treatment points were characterized for their chemical composition, bacterial abundance and for the abundance of four resistance genes against tetracycline, sulfonamides, erythromycin, and quinolones (tetA, sul2, ermB, and qnrS), and of the class 1 integrons (intI1). Although the chemical composition of the outflow significantly differed when the plant operated with or without industrial wastewater, the system efficiency in the removal of bacterial cells, ARGs, and intI1 was constant. The final disinfection by peracetic acid (PAA) did not affect the removal of ARGs, independently of the wastewater origin and the chemical characteristics of the inflows. Our results demonstrated that a well-functioning small size UWTP could treat a significant amount of industrial wastewater mixed in the urban sewage without affecting the overall ARGs and class 1 integrons released into the environment.

RevDate: 2018-09-20

De Mulder T, Rasschaert G, Van Coillie E, et al (2018)

Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in an Ex Vivo Model of the Pig's Cecum.

Microbial drug resistance (Larchmont, N.Y.) [Epub ahead of print].

AIMS: Cross-contamination of feed with antibiotics causes pigs to become unintentionally exposed to low concentrations of antibiotics. This study investigates the effect of residues of doxycycline hyclate (DOX) in an ex vivo model of the intestinal tract of pigs, focusing on the microbial community, microbial activity, and the enrichment of resistant bacteria and resistance genes.

RESULTS: The effect of three concentrations DOX were tested; 1 and 4 mg/L correspond to the intestinal concentrations when pigs are fed a compound feed containing 3% of a therapeutic dose, and a reference concentration of 16 mg/L. These were continuously administered to a chemostat, simulating the microbial ecosystem of the pig cecum and inoculated with cecal content of organically grown pigs. The administration of even the lowest DOX concentration caused a significant decrease in bacterial activity, while the microbial community profile appeared to remain unaffected by any of the concentrations. A concentration of 1 mg/L DOX caused minor selection pressure for tetracycline-resistant Escherichia coli but no other groups enumerated with plate cultivation, while 4 mg/L induced major enrichment of tetracycline-resistant E. coli, Enterobacteriaceae and total anaerobes. High abundances of tet(Q), tet(M), tet(W), tet(O), and tet(B) were detected in the inoculum and also before antibiotic administration in the chemostat and did not significantly increase during administration of 1 and 4 mg/L DOX. Only 16 mg/L DOX caused minor enrichments.

CONCLUSIONS: Cross-contamination concentrations of doxycycline, as a result of cross-contamination, cause a selection pressure for resistant bacteria and negatively affect microbial activity.

RevDate: 2018-09-20

Teurlincx S, Heijboer A, Veraart AJ, et al (2018)

Local Functioning, Landscape Structuring: Drivers of Soil Microbial Community Structure and Function in Peatlands.

Frontiers in microbiology, 9:2060.

Agricultural peatlands are essential for a myriad of ecosystem functions and play an important role in the global carbon (C) cycle through C sequestration. Management of these agricultural peatlands takes place at different spatial scales, ranging from local to landscape management, and drivers of soil microbial community structure and function may be scale-dependent. Effective management for an optimal biogeochemical functioning thus requires knowledge of the drivers on soil microbial community structure and functioning, as well as the spatial scales upon which they are influenced. During two field campaigns, we examined the importance of different drivers (i.e., soil characteristics, nutrient management, vegetation composition) at two spatial scales (local vs. landscape) for, respectively, the soil microbial community structure (determined by PLFA) and soil microbial community functional capacity (as assessed by CLPP) in agricultural peatlands. First, we show by an analysis of PLFA profiles that the total microbial biomass changes with soil moisture and relative C:P nutrient availability. Secondly, we showed that soil communities are controlled by a distinct set of drivers at the local, as opposed to landscape, scale. Community structure was found to be markedly different between areas, in contrast to community function which showed high variability within areas. We further found that microbial structure appears to be controlled more at a landscape scale by nutrient-related variables, whereas microbial functional capacity is driven locally through plant community feedbacks. Optimal management strategies within such peatlands should therefore consider the scale-dependent action of soil microbial community drivers, for example by first optimizing microbial structure at the landscape scale by targeted areal management, and then optimizing soil microbial function by local vegetation management.

RevDate: 2018-09-20

Ingala MR, Simmons NB, SL Perkins (2018)

Bats Are an Untapped System for Understanding Microbiome Evolution in Mammals.

mSphere, 3(5): pii:3/5/e00397-18.

Mammals evolved in a microbial world, and consequently, microbial symbionts have played a role in their evolution. An exciting new subdiscipline of metagenomics considers the ways in which microbes, particularly those found in the gut, have facilitated the ecological and phylogenetic radiation of mammals. However, the vast majority of such studies focus on domestic animals, laboratory models, or charismatic megafauna (e.g., pandas and chimpanzees). The result is a plethora of studies covering few taxa across the mammal tree of life, leaving broad patterns of microbiome function and evolution unclear. Wildlife microbiome research urgently needs a model system in which to test hypotheses about metagenomic involvement in host ecology and evolution. We propose that bats (Order: Chiroptera) represent a model system ideal for comparative microbiome research, affording opportunities to examine host phylogeny, diet, and other natural history characteristics in relation to the evolution of the gut microbiome.

RevDate: 2018-09-20

Malik A, Sharma D, Malireddi RKS, et al (2018)

SYK-CARD9 Signaling Axis Promotes Gut Fungi-Mediated Inflammasome Activation to Restrict Colitis and Colon Cancer.

Immunity, 49(3):515-530.e5.

Fungi represent a significant proportion of the gut microbiota. Aberrant immune responses to fungi are frequently observed in inflammatory bowel diseases (IBD) and colorectal cancer (CRC), and mutations in the fungal-sensing pathways are associated with the pathogenesis of IBD. Fungal recognition receptors trigger downstream signaling via the common adaptor protein CARD9 and the kinase SYK. Here we found that commensal gut fungi promoted inflammasome activation during AOM-DSS-induced colitis. Myeloid cell-specific deletion of Card9 or Syk reduced inflammasome activation and interleukin (IL)-18 maturation and increased susceptibility to colitis and CRC. IL-18 promoted epithelial barrier restitution and interferon-γ production by intestinal CD8+ T cells. Supplementation of IL-18 or transfer of wild-type myeloid cells reduced tumor burden in AOM-DSS-treated Card9-/- and Sykfl/flLysMCre/+ mice, whereas treatment with anti-fungal agents exacerbated colitis and CRC. CARD9 deletion changes the gut microbial landscape, suggesting that SYK-CARD9 signaling maintains a microbial ecology that promotes inflammasome activation and thereby restrains colitis and colon tumorigenesis.

RevDate: 2018-09-20

Vavourakis CD, Andrei AS, Mehrshad M, et al (2018)

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.

Microbiome, 6(1):168 pii:10.1186/s40168-018-0548-7.

BACKGROUND: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.

RESULTS: We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.

CONCLUSIONS: Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.

RevDate: 2018-09-19

Wu T, Grootaert C, Pitart J, et al (2018)

Aronia (Aronia melanocarpa) Polyphenols Modulate Microbial Community in Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) and Decrease Secretion of Pro-Inflammatory Markers in a Caco-2/endothelial Cell Co-Culture Model.

Molecular nutrition & food research [Epub ahead of print].

SCOPE: To explore the mechanisms behind the health effects of Aronia (Aronia melanocarpa), the microbial community modulating and anti-inflammatory effects of Aronia polyphenols were investigated by combining SHIME® with a co-culture of intestinal and endothelial cells.

RESULTS: Administration of Aronia juice (6.5g/L) to the SHIME® for 2 weeks increased the abundance of Firmicutes to 92% in AC, 85% in TC and 82% in DC(p < 0.001), Proteobacteria(6.7% in AC, p < 0.001) and Akkermansia (14% in TC and 18% in DC, p < 0.001) and decreased the abundance of Bifidobacterium species, associated with a decrease of acetate and increase of propionate and butyrate, whereas no significant difference was observed upon placebo juice treatment. After addition of the digests to TNF-α challenged Caco-2/endothelial co-cultures, ICAM-1, IL-8 and MCP-1 levels were significantly downregulated. Interestingly, Aronia juice treated digests from each colon compartments resulted in a stronger decrease of the ICAM-1 secretion (up to 73%, p < 0.001) compared to their corresponding placebo treated digests, thereby pointing to a polyphenol-dependent effect.

CONCLUSIONS: Aronia polyphenols modulate intestinal microbial composition, induce beneficial SCFA production and prevent inflammatory stress in endothelial cells. This opens perspectives for the use of Aronia polyphenols as prebiotics in the context of intestinal and cardiovascular health. This article is protected by copyright. All rights reserved.

RevDate: 2018-09-19

Ziller A, L Fraissinet-Tachet (2018)

Metallothionein diversity and distribution in the tree of life: a multifunctional protein.

Metallomics : integrated biometal science [Epub ahead of print].

MTs are small cysteine-rich proteins that chelate metal ions such as Cu+ and Zn2+, and are widely distributed in several life domains, in particular the eukaryotic one. They are present in the following phyla: Opisthokonta (mainly Fungi and Metazoa), Chloroplastida, Alveolata (ciliates) and Excavata (Trichomonas) for Eukaryota and Cyanobacteria, Actinobacteria, Proteobacteria and Firmicutes for Bacteria. However, their absence in some phyla underlines that MTs are far from being fully known. The MT amino acid sequences show a great diversity of sizes and structures both in terms of cysteine motifs and organization of these motifs. This review also highlights the different oxidized, apoprotein and metalated forms of MTs, the diversity of interactions they can establish with different molecules and their central and multifunctional cellular role. We present MTs as a protein system that could be a hub in molecular interaction networks. Studying MTs as a hub in cellular interaction networks should provide new insights for a better understanding of MT functioning and cellular processes.

RevDate: 2018-09-19

Gacesa R, Baranasic D, Starcevic A, et al (2018)

Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from 
Northern Adriatic Sea Sediments.

Food technology and biotechnology, 56(2):270-277.

Three metagenomic libraries were constructed using surface sediment samples from the northern Adriatic Sea. Two of the samples were taken from a highly polluted and an unpolluted site respectively. The third sample from a polluted site had been enriched using crude oil. The results of the metagenome analyses were incorporated in the REDPET relational database (, which was generated using the previously developed MEGGASENSE platform. The database includes taxonomic data to allow the assessment of the biodiversity of metagenomic libraries and a general functional analysis of genes using hidden Markov model (HMM) profiles based on the KEGG database. A set of 22 specialised HMM profiles was developed to detect putative genes for hydrocarbon-degrading enzymes. Use of these profiles showed that the metagenomic library generated after selection on crude oil had enriched genes for aerobic n-alkane degradation. The use of this system for bioprospecting was exemplified using potential alkB and almA genes from this library.

RevDate: 2018-09-19

Mechmeche M, Kachouri F, Ksontini H, et al (2018)

Bioprocess development and preservation of functional food from tomato seed isolate fermented by kefir culture mixture.

Journal of food science and technology, 55(10):3911-3921.

The aim of this work was to explore the use of protein isolate from tomato seed enriched with the sucrose and the ascorbic acid as a medium for the growth of kefir mixture culture to develop a new non-dairy functional food. Unstructured mathematical and logistic models were proposed to describe cell growth, kefiran production, nutriment consumption and antioxidant activity. It was found that the maximal cell mass in the culture reached 8.38 g L-1 after 24 h of fermentation. A significant amount of kefiran was also produced (0.65 g L-1). The kefir culture growth significantly decreased protein content and enhanced the antioxidant activity during varied fermentation through the production of bio active peptides. After 24 h of fermentation, IC50 value for protein isolate was estimated to be about 10.48 µg mL-1. The proposed models adequately described the changes during fermentation and as observed as a promising approach for the formulation of tomato seed-based functional foods. The preservation of the isolate was also investigated through a spray-drying process. The effect of spray-drying on the viability of lactic acid bacteria and stability of protein content and the antioxidant activity of the powder was also carried out. Results showed that the spray-drying method has great potential for the synthesis of powder from the fermented isolate that are rich in desirable properties. However, it was appropriate to preserve the powder for 10 days at 37 °C for the preservation of protein functionality.

RevDate: 2018-09-18

Sitaraman R (2018)

Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.

Microbiome, 6(1):163 pii:10.1186/s40168-018-0551-z.

The ubiquity of horizontal gene transfer in the living world, especially among prokaryotes, raises interesting and important scientific questions regarding its effects on the human holobiont i.e., the human and its resident bacterial communities considered together as a unit of selection. Specifically, it would be interesting to determine how particular gene transfer events have influenced holobiont phenotypes in particular ecological niches and, conversely, how specific holobiont phenotypes have influenced gene transfer events. In this synthetic review, we list some notable and recent discoveries of horizontal gene transfer among the prokaryotic component of the human microbiota, and analyze their potential impact on the holobiont from an ecological-evolutionary viewpoint. Finally, the human-Helicobacter pylori association is presented as an illustration of these considerations, followed by a delineation of unresolved questions and avenues for future research.

RevDate: 2018-09-18

Endo A, Maeno S, Tanizawa Y, et al (2018)

Fructophilic Lactic Acid Bacteria, a Unique Group of Fructose-Fermenting Microbes.

Applied and environmental microbiology, 84(19): pii:AEM.01290-18.

Fructophilic lactic acid bacteria (FLAB) are a recently discovered group, consisting of a few Fructobacillus and Lactobacillus species. Because of their unique characteristics, including poor growth on glucose and preference of oxygen, they are regarded as "unconventional" lactic acid bacteria (LAB). Their unusual growth characteristics are due to an incomplete gene encoding a bifunctional alcohol/acetaldehyde dehydrogenase (adhE). This results in the imbalance of NAD/NADH and the requirement of additional electron acceptors to metabolize glucose. Oxygen, fructose, and pyruvate are used as electron acceptors. FLAB have significantly fewer genes for carbohydrate metabolism than other LAB, especially due to the lack of complete phosphotransferase system (PTS) transporters. They have been isolated from fructose-rich environments, including flowers, fruits, fermented fruits, and the guts of insects that feed on plants rich in fructose, and are separated into two groups on the basis of their habitats. One group is associated with flowers, grapes, wines, and insects, and the second group is associated with ripe fruits and fruit fermentations. Species associated with insects may play a role in the health of their host and are regarded as suitable vectors for paratransgenesis in honey bees. Besides their impact on insect health, FLAB may be promising candidates for the promotion of human health. Further studies are required to explore their beneficial properties in animals and humans and their applications in the food industry.

RevDate: 2018-09-15

Zhang X, Prévoteau A, Louro RO, et al (2018)

Periodic polarization of electroactive biofilms increases current density and charge carriers concentration while modifying biofilm structure.

Biosensors & bioelectronics, 121:183-191 pii:S0956-5663(18)30645-6 [Epub ahead of print].

Anodic electroactive biofilms (EABs) need to overcome low current densities for applications such as microbial fuel cells or biosensors. EABs can store charge in self-produced redox proteins when temporarily left in open circuit, and discharge them once the electrode is appropriately repolarized, thus behaving as pseudocapacitors. Here we investigated the effect of such periodic polarization on the intrinsic nature of the EABs during their entire growth (i.e. starting from inoculation and for 10 days) on glassy carbon electrodes. An optimal periodic polarization (half-period of 10 s) greatly increased the maximum steady-state current density delivered by the Geobacter-dominated EABs (up to 1.10 ± 0.02 mA cm-2, n = 3 electrodes) when compared to continuously polarized EABs (0.41 ± 0.04 mA cm-2); and increased the amount of electric charges produced per hour by 69 ± 17% even taking into account the half-periods of open circuit. This enhancement was highly correlated with a substantial increase in charge carriers concentration (10.6 ± 0.5 mMe- vs. 2.9 ± 0.6 mMe-), allowing higher charge storage capacity and higher electron mobility across the EABs. Our results suggest that appropriate periodic polarizations may upregulate the expression of heme-containing redox proteins associated with the matrix, such as c-type cytochromes. The EABs grown under periodic polarization presented mushroom-like structures on their top layers, while EABs grown under continuous polarization were flat.

RevDate: 2018-09-15

Bernasconi R, Stat M, Koenders A, et al (2018)

Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont.

Microbial ecology pii:10.1007/s00248-018-1255-4 [Epub ahead of print].

Scleractinian corals form the framework of coral reefs and host abundant and diverse microbial communities that are fundamental to their success. A very limited number of studies have examined the co-occurrence of multiple partners within the coral 'holobiont' and their pattern of specificity over different geographical scales. In this study, we explored two molecular sequence datasets representing associations between corals and dinoflagellates in the genus Symbiodinium and between corals and bacteria, across the globe. Through a network theory approach, we characterised patterns of co-occurrences between bacteria and Symbiodinium with 13 coral genera across six water basins. The majority of the bacteria-Symbiodinium co-occurrences were specific to either a coral genus or water basin, emphasising both coral host and environment as important factors driving the diversity of coral assemblages. Yet, results also identified bacteria and Symbiodinium that were shared by multiple coral genera across several water basins. The analyses indicate that shared co-occurrences are independent of the phylogenetic and biogeographic relationship of coral hosts.

RevDate: 2018-09-15

Biswas S, Mukherjee P, Manna T, et al (2018)

Quorum Sensing Autoinducer(s) and Flagellum Independently Mediate EPS Signaling in Vibrio cholerae Through LuxO-Independent Mechanism.

Microbial ecology pii:10.1007/s00248-018-1262-5 [Epub ahead of print].

Vibrio cholerae, the Gram-negative bacterium causing lethal diarrheal disease cholera, forms biofilm on solid surfaces to gain adaptive advantage for successful survival in aquatic reservoirs. Expression of exopolysaccharide (EPS), an extracellular matrix material, has been found critical for biofilm-based environmental persistence. In a subset of epidemic-causing V. cholerae, absence of flagellum but not motility was identified to induce elevated exopolysaccharide expression. Identification of the role played by quorum sensing autoinducer molecules, i.e., cholera autoinducer 1 (CAI-1) and autoinducer 2 (AI-2) as well as central regulator LuxO on EPS expression in the subset was explored. Deletion mutations were introduced in vital genes responsible for synthesizing CAI-1 (cqsA), AI-2 (luxS), flagellum (flaA), LuxO (luxO), flagellar motor (motX), and VpsR (vpsR) in the model strain MO10. Subsequent phenotypic alterations in terms of colony morphology, EPS expression, biofilm formation, and transcription level of relevant genes were analyzed. Autoinducer cross-feeding experiment confirmed the role of autoinducers in EPS signaling. Results reveal that autoinducers and flagellum are the two major EPS signaling units in this subset where one unit becomes predominant for EPS production in absence of the other. Moreover, either unit exerts negative influence on EPS induction by the other. Both the EPS signaling cascades are independent of LuxO contribution and essentially involve sodium-driven flagellar motor and VpsR. A cell density and flagellum-mediated, but LuxO-independent, EPS signaling mechanism is considered to be functional in these organisms that confers their survival fitness.

RevDate: 2018-09-15

Mbareche H, Veillette M, Bilodeau GJ, et al (2018)

Bioaerosol Sampler Choice Should Consider Efficiency and Ability of Samplers to Cover Microbial Diversity.

Applied and environmental microbiology pii:AEM.01589-18 [Epub ahead of print].

Bioaerosol studies tend to describe the microbial content and understand the aerosolization processes linked to diseases. Air samplers are used to collect, identify and quantify bioaerosols. Studies comparing the performance of air samplers have typically used a culture approach or have targeted a specific microorganism in laboratory settings. The objective of this study was to use environmental field samples to compare the efficiency of 3 high airflow rate samplers for describing bioaerosol diversity using a next-generation sequencing approach. Two liquid cyclonic impactors and one electrostatic filter dry sampler were used in four wastewater treatment plants to target bacterial diversity and in five dairy farms to target fungal diversity. The dry electrostatic sampler was consistently more powerful in collecting more fungal and bacterial OTUs. Substantial differences in OTU abundance between liquid and dry sampling were revealed. The majority of the diversity revealed by dry electrostatic sampling was not identified using the cyclonic liquid impactors. The findings on this work suggest that the choice of a bioaerosol sampler should include information about the efficiency and ability of samplers to cover microbial diversity. Although these results suggest that electrostatic filters result in better coverage of the microbial diversity amongst the tested air samplers, further studies are needed to confirm this hypothesis. While it is difficult to determine a single universally optimal air sampler, this work provides an in-depth look at some of the considerations that are essential when choosing an air sampler for studying the microbial ecology of bioaerosols.Importance Associating bioaerosol exposure and health problems is challenging and adequate exposure monitoring is a priority for scientist in the field. Conclusions that can be drawn from bioaerosol exposure studies are highly dependent on the design of the study and the methodologies used. The air sampling strategy is the first methodological step leading to an accurate interpretation of what is present in the air. Applying new molecular approaches to evaluate the efficiency of the different types of samplers used in the field is a necessary work around the traditional approaches and the biases they introduce to such studies. The results and conclusions provided in this manuscript should be taken in considerations when conducting a bioaerosol study.

RevDate: 2018-09-14

Lindeboom REF, Ilgrande C, Carvajal-Arroyo JM, et al (2018)

Nitrogen cycle microorganisms can be reactivated after Space exposure.

Scientific reports, 8(1):13783 pii:10.1038/s41598-018-32055-4.

Long-term human Space missions depend on regenerative life support systems (RLSS) to produce food, water and oxygen from waste and metabolic products. Microbial biotechnology is efficient for nitrogen conversion, with nitrate or nitrogen gas as desirable products. A prerequisite to bioreactor operation in Space is the feasibility to reactivate cells exposed to microgravity and radiation. In this study, microorganisms capable of essential nitrogen cycle conversions were sent on a 44-days FOTON-M4 flight to Low Earth Orbit (LEO) and exposed to 10-3-10-4 g (gravitational constant) and 687 ± 170 µGy (Gray) d-1 (20 ± 4 °C), about the double of the radiation prevailing in the International Space Station (ISS). After return to Earth, axenic cultures, defined and reactor communities of ureolytic bacteria, ammonia oxidizing archaea and bacteria, nitrite oxidizing bacteria, denitrifiers and anammox bacteria could all be reactivated. Space exposure generally yielded similar or even higher nitrogen conversion rates as terrestrial preservation at a similar temperature, while terrestrial storage at 4 °C mostly resulted in the highest rates. Refrigerated Space exposure is proposed as a strategy to maximize the reactivation potential. For the first time, the combined potential of ureolysis, nitritation, nitratation, denitrification (nitrate reducing activity) and anammox is demonstrated as key enabler for resource recovery in human Space exploration.

RevDate: 2018-09-14

Lee K, Yu H, Zhang X, et al (2018)

Quorum sensing and quenching in membrane bioreactors: Opportunities and challenges for biofouling control.

Bioresource technology pii:S0960-8524(18)31264-1 [Epub ahead of print].

Membrane biofouling, due to biofilm growth after planktonic bacteria attachment to a membrane, is a major bottleneck limiting the energy-efficient operation and maintenance of membrane bioreactors (MBRs). Microbial communications, known as quorum sensing (QS), are responsible for this biofouling behavior. Novel strategies for stopping this communication, known as quorum quenching (QQ), appear to be successful for biofouling control in MBRs used for wastewater treatment. This review describes recent information regarding the signal molecules and mechanisms responsible for QS behaviors, promising approaches for QQ (enzymatic, bacterial, fungal, photocatalytic, mimicking, and biostimulating methods), and efficient fabrication and use of QQ media for MBR applications. We discuss the opportunities and challenges of QQ techniques for their further improvement and practical use in MBRs.

RevDate: 2018-09-13

Nguyen NL, Yu WJ, Gwak JH, et al (2018)

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils.

Frontiers in microbiology, 9:1982.

Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.

RevDate: 2018-09-13

Hernández-Gómez O, Briggler JT, RN Williams (2018)

Captivity-Induced Changes in the Skin Microbial Communities of Hellbenders (Cryptobranchus alleganiensis).

Microbial ecology pii:10.1007/s00248-018-1258-1 [Epub ahead of print].

Variation in environmental conditions can result in disparate associations between hosts and microbial symbionts. As such, it is imperative to evaluate how environmental variables (e.g., habitat quality) can influence host-associated microbiome composition. Within wildlife conservation programs, captive conditions can negatively influence the establishment and maintenance of "wild-type" microbiotas within a host. Alternative microbial communities can result in the proliferation of disease among captive stock or upon reintroduction. Hellbenders (Cryptobranchus alleganiensis) are a threatened salamander for which extensive captive management is currently employed. Using metabarcoding, we characterized the skin microbiota of wild and captive hellbenders from two subspecies in the state of Missouri, the eastern (C. a. alleganiensis) and the Ozark hellbender (C. a. bishopi). Both subspecies in our study included wild adults and captive juveniles that were collected from the wild as eggs. Our objectives were to investigate differences in the skin microbial communities' richness/diversity, composition, and functional profiles of microbes between wild and captive individuals. Captive eastern hellbenders possessed richer communities than wild cohorts, whereas the opposite pattern was observed within the Ozark subspecies. We found significant microbial community structure between wild and captive populations of both subspecies. Microbiota structure translated into differences in the predicted metagenome of wild and captive individuals as well. As such, we can expect captive hellbenders to experience alternative microbial structure and function upon reintroduction into the wild. Our study provides a baseline for the effect of captivity on the skin microbial communities of hellbenders, and highlights the need to incorporate microbiota management in current captive-rearing programs.

RevDate: 2018-09-13

Manjunatha BS, Paul S, Aggarwal C, et al (2018)

Diversity and Tissue Preference of Osmotolerant Bacterial Endophytes Associated with Pearl Millet Genotypes Having Differential Drought Susceptibilities.

Microbial ecology pii:10.1007/s00248-018-1257-2 [Epub ahead of print].

Genetic and functional diversity of osmotolerant bacterial endophytes colonizing the root, stem, and leaf tissues of pearl millet genotypes differing in their drought susceptibility was assessed. Two genotypes of pearl millet, viz., the drought tolerant genotype TT-1 and the drought susceptible genotype PPMI-69, were used in the present study. Diazotrophs were found to be the predominant colonizers, followed by the Gram positive bacteria in most of the tissues of both the genotypes. Higher proportion of bacterial endophytes obtained from the drought tolerant genotype was found to be osmotolerant. Results of 16S rRNA gene-ARDRA analysis grouped 50 of the highly osmotolerant isolates into 16 clusters, out of which nine clusters had only one isolate each, indicating their uniqueness. One cluster had 21 isolates and remaining clusters were represented by isolates ranging from two to four. The representative isolates from each cluster were identified, and Bacillus was found to be the most prevalent osmotolerant genera with many different species. Other endophytic bacteria belonged to Pseudomonas sp., Stenotrophomonas sp., and Macrococcus caseolyticus. High phylogenetic diversity was observed in the roots of the drought tolerant genotype while different tissues of the drought susceptible genotype showed less diversity. Isolates of Bacillus axarquiensis were present in all the tissues of both the genotypes of pearl millet. However, most of the other endophytic bacteria showed tissue/genotype specificity. With the exception of B. axarquiensis and B. thuringiensis, rest all the species of Bacillus were found colonizing only the drought-tolerant genotype; while M. caseolyticus colonized all the tissues of only the drought susceptible genotype. There was high incidence of IAA producers and low incidence of ACC deaminase producers among the isolates from the root tissues of the drought-tolerant genotype while reverse was the case for the drought-susceptible genotype. Thus, host played an important role in the selection of endophytes based on both phylogenetic and functional traits.

RevDate: 2018-09-13

Houfani AA, Větrovský T, Navarrete OU, et al (2018)

Cellulase-Hemicellulase Activities and Bacterial Community Composition of Different Soils from Algerian Ecosystems.

Microbial ecology pii:10.1007/s00248-018-1251-8 [Epub ahead of print].

Soil microorganisms are important mediators of carbon cycling in nature. Although cellulose- and hemicellulose-degrading bacteria have been isolated from Algerian ecosystems, the information on the composition of soil bacterial communities and thus the potential of their members to decompose plant residues is still limited. The objective of the present study was to describe and compare the bacterial community composition in Algerian soils (crop, forest, garden, and desert) and the activity of cellulose- and hemicellulose-degrading enzymes. Bacterial communities were characterized by high-throughput 16S amplicon sequencing followed by the in silico prediction of their functional potential. The highest lignocellulolytic activity was recorded in forest and garden soils whereas activities in the agricultural and desert soils were typically low. The bacterial phyla Proteobacteria (in particular classes α-proteobacteria, δ-proteobacteria, and γ-proteobacteria), Firmicutes, and Actinobacteria dominated in all soils. Forest and garden soils exhibited higher diversity than agricultural and desert soils. Endocellulase activity was elevated in forest and garden soils. In silico analysis predicted higher share of genes assigned to general metabolism in forest and garden soils compared with agricultural and arid soils, particularly in carbohydrate metabolism. The highest potential of lignocellulose decomposition was predicted for forest soils, which is in agreement with the highest activity of corresponding enzymes.

RevDate: 2018-09-13

Shade A, Dunn RR, Blowes SA, et al (2018)

Macroecology to Unite All Life, Large and Small.

Trends in ecology & evolution pii:S0169-5347(18)30186-1 [Epub ahead of print].

Macroecology is the study of the mechanisms underlying general patterns of ecology across scales. Research in microbial ecology and macroecology have long been detached. Here, we argue that it is time to bridge the gap, as they share a common currency of species and individuals, and a common goal of understanding the causes and consequences of changes in biodiversity. Microbial ecology and macroecology will mutually benefit from a unified research agenda and shared datasets that span the entirety of the biodiversity of life and the geographic expanse of the Earth.

RevDate: 2018-09-12

Kispal ZF, Vajda P, Kardos D, et al (2018)

The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota.

Journal of pediatric urology pii:S1477-5131(18)30440-6 [Epub ahead of print].

INTRODUCTION: Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown.

OBJECTIVE: The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS.

STUDY DESIGN: Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso.

RESULTS: Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (β-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on β-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients.

CONCLUSION: After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.

RevDate: 2018-09-11

Lee JZ, Everroad RC, Karaoz U, et al (2018)

Metagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.

PloS one, 13(9):e0202792 pii:PONE-D-18-09048.

Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.

RevDate: 2018-09-10

Dolan JR (2018)

The Villefranche Strombidium sulcatum: A review.

European journal of protistology, 66:68-76 pii:S0932-4739(18)30064-6 [Epub ahead of print].

The marine oligotrich ciliate Strombidium sulcatum, the best known marine oligotrich of the marine microozoplankton, was first cultured in Villefranche-sur-Mer 35 years ago. Cultures were maintained from 1983 to 2003 and used in 22 studies investigating a very wide variety of questions. Here we review the major findings of these studies and underline their contributions to our knowledge of planktonic ciliate ecology and microbial ecology in general. We conclude with the observation that while ecophysiology has apparently fallen out of fashion, culture work will likely return as an invaluable resource in our present 'omics' era.

RevDate: 2018-09-10

Couper L, A Swei (2018)

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing.

Journal of visualized experiments : JoVE.

In recent decades, vector-borne diseases have re-emerged and expanded at alarming rates, causing considerable morbidity and mortality worldwide. Effective and widely available vaccines are lacking for a majority of these diseases, necessitating the development of novel disease mitigation strategies. To this end, a promising avenue of disease control involves targeting the vector microbiome, the community of microbes inhabiting the vector. The vector microbiome plays a pivotal role in pathogen dynamics, and manipulations of the microbiome have led to reduced vector abundance or pathogen transmission for a handful of vector-borne diseases. However, translating these findings into disease control applications requires a thorough understanding of vector microbial ecology, historically limited by insufficient technology in this field. The advent of next-generation sequencing approaches has enabled rapid, highly parallel sequencing of diverse microbial communities. Targeting the highly-conserved 16S rRNA gene has facilitated characterizations of microbes present within vectors under varying ecological and experimental conditions. This technique involves amplification of the 16S rRNA gene, sample barcoding via PCR, loading samples onto a flow cell for sequencing, and bioinformatics approaches to match sequence data with phylogenetic information. Species or genus-level identification for a high number of replicates can typically be achieved through this approach, thus circumventing challenges of low detection, resolution, and output from traditional culturing, microscopy, or histological staining techniques. Therefore, this method is well-suited for characterizing vector microbes under diverse conditions but cannot currently provide information on microbial function, location within the vector, or response to antibiotic treatment. Overall, 16S next-generation sequencing is a powerful technique for better understanding the identity and role of vector microbes in disease dynamics.

RevDate: 2018-09-10

Mise K, Fujita K, Kunito T, et al (2018)

Phosphorus-mineralizing Communities Reflect Nutrient-Rich Characteristics in Japanese Arable Andisols.

Microbes and environments [Epub ahead of print].

Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 arable Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types.

RevDate: 2018-09-10

Šulčius S, Mazur-Marzec H, Vitonytė I, et al (2018)

Insights into cyanophage-mediated dynamics of nodularin and other non-ribosomal peptides in Nodularia spumigena.

Harmful algae, 78:69-74.

The effect of cyanophage infection and lysis on the dynamics of the hepatotoxin nodularin (NOD) and other non-ribosomal peptides (NRPs) produced by cyanobacteria is poorly understood. In this study, changes in concentration of NOD and other NRPs during cyanophage infection of the filamentous cyanobacteria Nodularia spumigena were assessed using incubation experiments. Viral infection and lysis were associated with a significant reduction (93% at the 96 h post infection) of N. spumigena cell density. While no correlation between N. spumigena abundance and total concentration of NOD (ng mL-1) within the infected cells was observed, cellular NOD quota (ng cell-1) gradually increased in the remaining cyanophage resistant N. spumigena subpopulation. Lysis of N. spumigena cells resulted in a substantial increase (>57 times) of dissolved NOD concentration in the culture medium. The relative concentration of other cyclic (anabaenopeptins) and linear (aeruginosins, spumigins) NRPs produced by N. spumigena also increased in response to cyanophage addition. This study highlights the importance of cyanophage infection on the population toxicity of filamentous cyanobacteria and demonstrates a significant contribution of virus-mediated cell lysis on the conversion of NOD from the particulate to dissolved phase.

RevDate: 2018-09-10

Bittleston LS, Wolock CJ, Yahya BE, et al (2018)

Convergence between the microcosms of Southeast Asian and North American pitcher plants.

eLife, 7: pii:36741.

The 'pitchers' of carnivorous pitcher plants are exquisite examples of convergent evolution. An open question is whether the living communities housed in pitchers also converge in structure or function. Using samples from more than 330 field-collected pitchers of eight species of Southeast Asian Nepenthes and six species of North American Sarracenia, we demonstrate that the pitcher microcosms, or miniature ecosystems with complex communities, are strikingly similar. Compared to communities from surrounding habitats, pitcher communities house fewer species. While communities associated with the two genera contain different microbial organisms and arthropods, the species are predominantly from the same phylogenetic clades. Microbiomes from both genera are enriched in degradation pathways and have high abundances of key degradation enzymes. Moreover, in a manipulative field experiment, Nepenthes pitchers placed in a North American bog assembled Sarracenia-like communities. An understanding of the convergent interactions in pitcher microcosms facilitates identification of selective pressures shaping the communities.

RevDate: 2018-09-09

Ullah A, Akbar A, Luo Q, et al (2018)

Microbiome Diversity in Cotton Rhizosphere Under Normal and Drought Conditions.

Microbial ecology pii:10.1007/s00248-018-1260-7 [Epub ahead of print].

Climate change contributes to drought stress and subsequently affects crop growth, development, and yield. The microbial community, such as fungi and bacteria in the rhizosphere, is of special importance to plant productivity. In this study, soil collected from a cotton research field was used to grow cotton plants (Gossypium hirsutum cv. Jin668) under controlled environment conditions. Drought stress was applied at flowering stage, while control plants were regularly watered. At the same time, the soil without plants was also subjected to drought, while control pots were regularly watered. The soil was collected in sterilized tubes and microbial DNA was isolated and high-throughput sequencing of 16S rRNA genes was carried out. The alpha diversity of bacteria community significantly increased in the soil with cotton plants compared to the soil without cotton plants. Taxonomic analysis revealed that the bacterial community structure of the cotton rhizosphere predominantly consisted of the phyla Proteobacteria (31.7%), Actinobacteria (29.6%), Gemmatimonadetes (9.8%), Chloroflexi (9%), Cyanobacteria (5.6%), and Acidobacteria. In the drought-treated rhizosphere, Chloroflexi and Gemmatimonadetes were the dominant phyla. This study reveals that the cotton rhizosphere has a rich pool of bacterial communities even under drought stress, and which may improve drought tolerance in plants. These data will underpin future improvement of drought tolerance of cotton via the soil microbial community.

RevDate: 2018-09-09

Jamar G, Santamarina AB, Dias GC, et al (2018)

Relationship between fatty acids intake and Clostridium coccoides in obese individuals with metabolic syndrome.

Food research international (Ottawa, Ont.), 113:86-92.

Dietary habits exert a strong influence on gut microbial composition and may result in an imbalance of gut microbes, representing a predisposition to obesity and metabolic disorders. We aimed to investigate a potential relationship between gut bacterial species and metabolic parameters and dietary intake. Bacterial DNA was extracted from feces of 34 obese subjects with and without metabolic syndrome (MS and n-MS group, respectively). We then used real-time polymerase chain reaction (qPCR) for quantifying specific sequences to Akkermansia muciniphila, Bifidobacterium spp., Clostridium coccoides, and Lactobacillus spp. and analyzed them with respect to clinical characteristics. Our data showed that the MS group had a 6.7-fold higher level of C. coccoides in their stool samples than the n-MS group. The abundance of C. coccoides was positively correlated with a high intake of monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids. Furthermore, an excessive dietary level of MUFA was identified as a predictor of C. coccoides abundance. Alterations in the gut microbial ecology were positively correlated with levels of triacylglycerol in obese individuals. Therefore, the type and quantity of dietary fat may alter the gut microbial ecology in obese individuals with MS and may predispose them to dyslipidemia.

RevDate: 2018-09-09

Nash V, Ranadheera CS, Georgousopoulou EN, et al (2018)

The effects of grape and red wine polyphenols on gut microbiota - A systematic review.

Food research international (Ottawa, Ont.), 113:277-287.

There is a growing body of evidence implicating the gut 'microbiome' role in overall human health. Bacterial species belonging to the genera Lactobacillus and Bifidobacterium are generally considered to be beneficial and are commonly used in probiotic applications, whereas increases in some genera including Clostridum, Eubacterium and Bacteroides are implicated in negative health outcomes. Dietary polyphenols are bioactive compounds that have been found to increase the numbers of beneficial bacteria and antimicrobial actions against pathogenic bacteria, however most studies have been conducted in animal models or in-vitro colonic models. The aim of this systematic review was to provide an overview of recent trials on the effect of dietary grape and red wine polyphenols on the gut microbiota in humans. Following PRISMA guidelines, a systematic review was conducted of electronic databases (PubMed, CINAHL, Cochrane Library, Wed of Science and Scopus) to identify human intervention trials examining the effect of grape or wine polyphenols on gut microbiota. Seven trials met the inclusion criteria. One study looked at changes in gut microbiota following the ingestion of de-alcoholised red wine or red wine, and six studies referred to gut microbiota as intermediates in formation of phenolic metabolites. All studies confirmed that ingested polyphenols from grape and red wine, were modulated by gut microbiota, increasing numbers of polyphenolic metabolites which were found in blood, urine, ileal fluid and faeces. Intake of polyphenols derived from grape and red wine can modulate gut microbiota and contribute to beneficial microbial ecology that can enhance human health benefits. Additionally, grape and red wine polyphenols were modulated by the gut microbiota and there is a potential for a two-way relationship between the gut microbiota and polyphenolic compounds. Nevertheless, additional research is required to fully understand the complex relationship between gut microbiota and dietary polyphenols before any health claims can be made in relation to human health.

RevDate: 2018-09-09

Medlock GL, Carey MA, McDuffie DG, et al (2018)

Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota.

Cell systems pii:S2405-4712(18)30318-1 [Epub ahead of print].

The diversity and number of species present within microbial communities create the potential for a multitude of interspecies metabolic interactions. Here, we develop, apply, and experimentally test a framework for inferring metabolic mechanisms associated with interspecies interactions. We perform pairwise growth and metabolome profiling of co-cultures of strains from a model mouse microbiota. We then apply our framework to dissect emergent metabolic behaviors that occur in co-culture. Based on one of the inferences from this framework, we identify and interrogate an amino acid cross-feeding interaction and validate that the proposed interaction leads to a growth benefit in vitro. Our results reveal the type and extent of emergent metabolic behavior in microbial communities composed of gut microbes. We focus on growth-modulating interactions, but the framework can be applied to interspecies interactions that modulate any phenotype of interest within microbial communities.

RevDate: 2018-09-08

da Silveira APD, Iório RPF, Marcos FCC, et al (2018)

Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition.

Antonie van Leeuwenhoek pii:10.1007/s10482-018-1157-y [Epub ahead of print].

Few studies have evaluated endophytic bacteria in relation to plant growth promotion, nitrogen uptake and biological control. The aim of this study was to molecularly and physiologically characterize thirteen endophytic bacteria strains, evaluate their biological control properties and their ability to promote plant growth and plant N nutrition. All the strains produced indole acetic acid and promoted increase of plant biomass, N accumulative amount and N-use efficiency index. None of the strains carries the nifH gene. Four strains stimulated plant nitrate reductase activity, four solubilized phosphate, nine produced siderophores and none produced HCN. Seven strains inhibited Bipolaris sacchari growth and one was antagonistic to Ceratocystis paradoxa. The pathogens were inhibited by the production of diffusible and volatile metabolites by the bacterial strains. Moreover, this is the first study to demonstrate the effect of Delftia acidovorans on sugarcane plant growth, nitrogen metabolism improvement and antagonism to B. sacchari. The most efficient strains in promoting plant growth and exhibiting antagonistic activities towards fungal pathogens were Herbaspirillum frinsingense (IAC-BECa-152) and three Pantoea dispersa strains (IAC-BECa-128, IAC-BECa-129, and IAC-BECa-132). These bacteria show potential to be used as inoculants for sustainable agricultural management, mainly at the seedling production phase.

RevDate: 2018-09-08

Szubert-Kruszyńska A, Stańczak J, Cieniuch S, et al (2018)

Correction to: Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.

The original version of this article published online (27 August 2018) unfortunately contained a mistake regarding an affiliation of Dr. Edyta Podsiadły, one of the authors.

RevDate: 2018-09-08

Eichmeier A, Kiss T, Necas T, et al (2018)

High-Throughput Sequencing Analysis of the Bacterial Community in Stone Fruit Phloem Tissues Infected by "Candidatus Phytoplasma prunorum".

Microbial ecology pii:10.1007/s00248-018-1250-9 [Epub ahead of print].

"Candidatus Phytoplasma prunorum" (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.

RevDate: 2018-09-08

Cordovez V, Schop S, Hordijk K, et al (2018)

Priming of plant growth promotion by volatiles of root-associated Microbacterium.

Applied and environmental microbiology pii:AEM.01865-18 [Epub ahead of print].

Volatile compounds produced by plant-associated microorganisms represent a diverse resource to promote plant growth and health. Here we investigated the effect of volatiles from root-associated Microbacterium species on plant growth and development. Volatiles of eight strains induced significant increases in shoot and root biomass of Arabidopsis, but differed in their effects on root architecture. Microbacterium strain EC8 also enhanced root and shoot biomass of lettuce and tomato. Biomass increases were also observed for plants exposed only shortly to volatiles from EC8 prior to transplantation of the seedlings to soil. These results indicate that volatiles from EC8 can prime plants for growth promotion without direct and prolonged contact. We further showed that the induction of plant growth promotion is tissue specific: exposure of roots to volatiles from EC8 led to an increase in plant biomass whereas shoot exposure resulted in no or less growth promotion. GC-QTOF analysis revealed that EC8 produces a wide array of sulfur containing compounds as well as ketones. Bioassays with synthetic sulfur volatile compounds revealed that the plant growth response to dimethyl trisulfide was concentration-dependent with a significant increase in shoot weight at 1 μM and negative effects on plant biomass at concentrations higher than 1 mM. Genome-wide transcriptome analysis of volatile-exposed Arabidopsis seedlings showed up-regulation of genes involved in assimilation and transport of sulfate and nitrate. Collectively, these results show that root-associated Microbacterium primes plants, via the roots, for growth promotion most likely via modulation of sulfur and nitrogen metabolism.Importance In the past decade, various studies have described the effects of microbial volatiles on other (micro)organisms in vitro, but their broad-spectrum activity in vivo and the mechanisms underlying volatile-mediated plant growth promotion have not been addressed in detail. Here, we revealed that volatiles from root-associated bacteria of the genus Microbacterium can enhance growth of different plant species and can prime plants for growth promotion without direct and prolonged contact between the bacterium and the plant. Collectively, these results provide new opportunities for sustainable agriculture and horticulture by exposing roots of plants only briefly to a specific blend of microbial volatile compounds prior to transplantation of the seedlings to the greenhouse or field. This strategy has no need for large-scale introduction, root colonization and survival of the microbial inoculant.

RevDate: 2018-09-07

Borel N, Bavoil P, Greub G, et al (2018)

International Committee on Systematics of Prokaryotes Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 9 April 2017, Charlotte, USA.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

RevDate: 2018-09-07

Tarnecki AM, Brennan NP, Schloesser RW, et al (2018)

Shifts in the Skin-Associated Microbiota of Hatchery-Reared Common Snook Centropomus undecimalis During Acclimation to the Wild.

Microbial ecology pii:10.1007/s00248-018-1252-7 [Epub ahead of print].

The skin-associated microbiota of fish competes against pathogens for space and nutrients, preventing colonization by harmful bacteria encountered during environmental transitions such as those faced during stock enhancement. Thus, alterations in bacterial community structure during release of cultured fish have important implications for health of these individuals. This study investigated microbiota structure during acclimation of juvenile hatchery-reared common snook Centropomus undecimalis to the wild by comparing skin-associated microflora among snook in captivity, after 48 h of acclimation at release sites, and from the wild. After two days of acclimation, the microbiota of hatchery-reared snook mirrored that observed on wild snook. Relative abundances of potential pathogens were higher in captive fish, whereas acclimated and wild fish harbored bacterial taxa influenced by geographical factors and water quality at release sites. Predicted microbiota function of acclimated and wild fish showed higher production of protective amino acids and antimicrobials, identifying a mechanism for microbial supplementation of the immune defense of these fish. The two-day transition to wild-type microbiota suggests a temporal scale of hours associated with bacterial succession indicating that the microbiota, whose structure is vital to fish health, aids in acclimation of fish to new environments during stock enhancement efforts.

RevDate: 2018-09-07

Safonov AV, Babich TL, Sokolova DS, et al (2018)

Microbial Community and in situ Bioremediation of Groundwater by Nitrate Removal in the Zone of a Radioactive Waste Surface Repository.

Frontiers in microbiology, 9:1985.

The goal of the present work was to investigate the physicochemical and radiochemical conditions and the composition of the microbial community in the groundwater of a suspended surface repository for radioactive waste (Russia) and to determine the possibility of in situ groundwater bioremediation by removal of nitrate ions. Groundwater in the repository area (10-m depth) had elevated concentrations of strontium, tritium, nitrate, sulfate, and bicarbonate ions. High-throughput sequencing of the V3-V4/V4 region of the 16S rRNA gene revealed the presence of members of the phyla Proteobacteria (genera Acidovorax, Simplicispira, Thermomonas, Thiobacillus, Pseudomonas, Brevundimonas, and uncultured Oxalobacteraceae), Firmicutes (genera Bacillus and Paenibacillus), and Actinobacteria (Candidatus Planktophila, Gaiella). Canonical correspondence analysis suggested that major contaminant - nitrate, uranium, and sulfate shaped the composition of groundwater microbial community. Groundwater samples contained culturable aerobic organotrophic, as well as anaerobic fermenting, iron-reducing, and denitrifying bacteria. Pure cultures of 33 bacterial strains belonging to 15 genera were isolated. Members of the genera Pseudomonas, Rhizobium, Cupriavidus, Shewanella, Ensifer, and Thermomonas reduced nitrate to nitrite and/or dinitrogen. Application of specific primers revealed the nirS and nirK genes encoding nitrite reductases in bacteria of the genera Pseudomonas, Rhizobium, and Ensifer. Nitrate reduction by pure bacterial cultures resulted in decreased ambient Eh. Among the organic substrates tested, sodium acetate and milk whey were the best for stimulation of denitrification by the microcosms with groundwater microorganisms. Injection of these substrates into the subterranean horizon (single-well push-pull test) resulted in temporary removal of nitrate ions in the area of the suspended radioactive waste repository and confirmed the possibility for in situ application of this method for bioremediation.

RevDate: 2018-09-07

Hicks N, Liu X, Gregory R, et al (2018)

Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments.

Frontiers in microbiology, 9:1730.

Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.

RevDate: 2018-09-06

Shibl AA, Ngugi DK, Talarmin A, et al (2018)

The genome of a novel isolate of Prochlorococcus from the Red Sea contains transcribed genes for compatible solute biosynthesis.

FEMS microbiology ecology pii:5090968 [Epub ahead of print].

Marine microbes possess genomic and physiological adaptations to cope with varying environmental conditions. So far, the effects of high salinity on the most abundant marine photoautotrophic organism, Prochlorococcus, in marine oligotrophic environments are mostly unknown. Here, we report the isolation of a new Prochlorococcus strain (RSP50) belonging to high-light (HL) clade II from the Red Sea, one of the warmest and most saline bodies of water in the global ocean. A comparative genomic analysis identified a set of 59 genes that were exclusive to RSP50 relative to currently available Prochlorococcus genomes, the majority of which (70%) encode for hypothetical proteins of unknown function. However, three of the unique genes encode for a complete pathway for the biosynthesis of the compatible solute glucosylglycerol, and are homologous to enzymes found in the sister lineage Synechococcus. Metatranscriptomic analyses of this metabolic pathway in the water-column of the Red Sea revealed that the corresponding genes were constitutively transcribed, independent of depth and light, suggesting that osmoregulation using glucosylglycerol is a general feature of HL II Prochlorococcus in the Red Sea.

RevDate: 2018-09-06

Coats ER, Eyre K, Bryant C, et al (2018)

Assessing the Effects of RAS Fermentation on EBPR Performance and Associated Microbial Ecology.

Water environment research : a research publication of the Water Environment Federation, 90(7):659-671.

Enhanced biological phosphorus removal (EBPR) is an engineered water resource recovery facility (WRRF) process configuration that can produce effluent P < 0.5 mg/L. To consistently achieve low effluent P concentrations, EBPR requires volatile fatty acids (VFAs) to induce requisite biochemical reactions. Moreover, returned activated sludge (RAS) nitrate concentrations must be minimized. Returned activated sludge fermentation can potentially address process needs. However, research detailed herein highlights concerns with RAS fermentation integrated with EBPR. Under 2 and 4 hours of RAS fermentation periods, no consequential VFA production was observed; similar results were observed in batch tests with RAS from a full-scale EBPR WRRF. More critically, EBPR performance was poor, with average effluent concentrations of 1.0 to 2.4 mg/L. Furthermore, the glycogen accumulating organism (GAO) fraction under RAS fermentation was 4.3 to 8.7 times higher than in a conventional EBPR mixed microbial consortium (MMC). Integrated RAS fermentation-EBPR only performed well under "high" RAS nitrate; thus, should RAS fermentation be implemented, careful control to prevent anaerobic conditions in the fermentation zone is required.

RevDate: 2018-09-06

Hooper R, Brealey JC, van der Valk T, et al (2018)

Host-derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin.

Molecular ecology [Epub ahead of print].

Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated microorganisms. Whereas amplicon sequencing has traditionally been used to characterise the microbiome, the increasing number of published population genomics datasets offer an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies for population genomics, to characterise the skin microbiome and investigate how host social and geographic factors influence the microbial community composition. Having identified 845 microbial taxa from 2.4 million reads that did not map to the killer whale reference genome, we found that both ecotypic and geographic factors influence community composition of killer whale skin microbiomes. Furthermore, we uncovered key taxa that drive the microbiome community composition and showed that they are embedded in unique networks, one of which is tentatively linked to diatom presence and poor skin condition. Community composition differed between Antarctic killer whales with and without diatom coverage, suggesting that the previously reported episodic migrations of Antarctic killer whales to warmer waters associated with skin turnover may control the effects of potentially pathogenic bacteria such as Tenacibaculum dicentrarchi. Our work demonstrates the feasibility of microbiome studies from host shotgun sequencing data and highlights the importance of metagenomics in understanding the relationship between host and microbial ecology. This article is protected by copyright. All rights reserved.

RevDate: 2018-09-06

Chan YF, Chiang KP, Ku Y, et al (2018)

Abiotic and Biotic Factors Affecting the Ingestion Rates of Mixotrophic Nanoflagellates (Haptophyta).

Microbial ecology pii:10.1007/s00248-018-1249-2 [Epub ahead of print].

Mixotrophic haptophytes comprise one of several important groups of mixotrophic nanoflagellates in the pelagic environment. This study aimed to investigate if phagotrophy in mixotrophic haptophytes is regulated by light or other factors in the surface (SE) and bottom (BE) of the euphotic zone in the subtropical northwestern Pacific Ocean. We estimated the rates of bacterial ingestion by haptophytes using fluorescently labeled bacteria (FLBs) and fluorescence in situ hybridization. Haptophyte diversity and abundance were also investigated in the same sampling area. The annual mean abundance of haptophytes was 419 ± 85.6 cells mL-1 in both SE and BE. Cells 3-5 μm in size were the dominant group in all haptophytes and accounted for majority of bacteria standing stock removed by haptophytes (53%). Most haptophyte ingestion rates (IRs) were not significantly different between the two layers (average SE ingestion rate: 12.5 ± 2.29 bac Hap-1 h-1; BE: 14.7 ± 3.03 bac Hap-1 h-1). Furthermore, the haptophyte IRs were negatively correlated with nitrate concentrations in the SE and positively correlated with bacterial abundances in the BE, which accounts for the significantly high IRs in August 2012 and 2013. These findings imply that mixotrophic haptophytes in this region had different factors affecting phagotrophy to adapt to the ambient light intensity alterations between SE and BE.

RevDate: 2018-09-06

Vallesi A, Sjödin A, Petrelli D, et al (2018)

A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species.

Microbial ecology pii:10.1007/s00248-018-1256-3 [Epub ahead of print].

The study of the draft genome of an Antarctic marine ciliate, Euplotes petzi, revealed foreign sequences of bacterial origin belonging to the γ-proteobacterium Francisella that includes pathogenic and environmental species. TEM and FISH analyses confirmed the presence of a Francisella endocytobiont in E. petzi. This endocytobiont was isolated and found to be a new species, named F. adeliensis sp. nov.. F. adeliensis grows well at wide ranges of temperature, salinity, and carbon dioxide concentrations implying that it may colonize new organisms living in deeply diversified habitats. The F. adeliensis genome includes the igl and pdp gene sets (pdpC and pdpE excepted) of the Francisella pathogenicity island needed for intracellular growth. Consistently with an F. adeliensis ancient symbiotic lifestyle, it also contains a single insertion-sequence element. Instead, it lacks genes for the biosynthesis of essential amino acids such as cysteine, lysine, methionine, and tyrosine. In a genome-based phylogenetic tree, F. adeliensis forms a new early branching clade, basal to the evolution of pathogenic species. The correlations of this clade with the other clades raise doubts about a genuine free-living nature of the environmental Francisella species isolated from natural and man-made environments, and suggest to look at F. adeliensis as a pioneer in the Francisella colonization of eukaryotic organisms.

RevDate: 2018-09-06

Olivares M, Schüppel V, Hassan AM, et al (2018)

The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health.

Frontiers in microbiology, 9:1900.

The Dipeptidyl peptidase-4 (DPP-4) activity influences metabolic, behavioral and intestinal disorders through the cleavage of key hormones and peptides. Some studies describe the existence of human DPP-4 homologs in commensal bacteria, for instance in Prevotella or Lactobacillus. However, the role of the gut microbiota as a source of DPP-4-like activity has never been investigated. Through the comparison of the DPP-4 activity in the cecal content of germ-free mice (GFM) and gnotobiotic mice colonized with the gut microbiota of a healthy subject, we bring the proof of concept that a significant DPP-4-like activity occurs in the microbiota. By analyzing the existing literature, we propose that DPP-4-like activity encoded by the intestinal microbiome could constitute a novel mechanism to modulate protein digestion as well as host metabolism and behavior.

RevDate: 2018-09-06

Rohwer RR, Hamilton JJ, Newton RJ, et al (2018)

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution.

mSphere, 3(5): pii:3/5/e00327-18.

Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set's sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source and is available at Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are data set dependent and cannot be compared between data sets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus, and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between data sets.

RevDate: 2018-09-05

Mangin I, Dossou-Yovo F, Lévêque C, et al (2018)

Oral administration of viable Bifidobacterium pseudolongum strain Patronus modified colonic microbiota and increased mucus layer thickness in rat.

FEMS microbiology ecology pii:5090401 [Epub ahead of print].

This study aimed at evaluating the alteration of the colonic microbiota and the changes in the mucus layer thickness induced by oral administration of living bifidobacteria in rats. The study was performed on rats fed with Bifidobacterium pseudolongum strain Patronus (1010 bacteria per day for 7 days). This bacterial administration led to a large increase of mucus thickness (57%, p<0.05). Both quantitative PCR and high-throughput sequencing of bacterial 16S rRNA gene revealed a significant increase of the amount of the Bifidobacterium genus in the microbiota of rats fed with the strain Patronus, associated with a decrease of Akkermansia muciniphila. The increase in mucus thickness could be due to an increase of the bifidobacteria per se or via the decrease of A. muciniphila, a major mucin-degrading species. As the mucus layer plays an essential role in gut protection, our data enlighten the importance of studying mucus-degrading bacteria for understanding the underlying etiology of diseases such as intestinal bowel diseases and to implement new therapeutic strategies.

RevDate: 2018-09-05

Castelle CJ, Brown CT, Anantharaman K, et al (2018)

Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations.

Nature reviews. Microbiology pii:10.1038/s41579-018-0076-2 [Epub ahead of print].

Candidate phyla radiation (CPR) bacteria and DPANN (an acronym of the names of the first included phyla) archaea are massive radiations of organisms that are widely distributed across Earth's environments, yet we know little about them. Initial indications are that they are consistently distinct from essentially all other bacteria and archaea owing to their small cell and genome sizes, limited metabolic capacities and often episymbiotic associations with other bacteria and archaea. In this Analysis, we investigate their biology and variations in metabolic capacities by analysis of approximately 1,000 genomes reconstructed from several metagenomics-based studies. We find that they are not monolithic in terms of metabolism but rather harbour a diversity of capacities consistent with a range of lifestyles and degrees of dependence on other organisms. Notably, however, certain CPR and DPANN groups seem to have exceedingly minimal biosynthetic capacities, whereas others could potentially be free living. Understanding of these microorganisms is important from the perspective of evolutionary studies and because their interactions with other organisms are likely to shape natural microbiome function.

RevDate: 2018-09-05

Evans SE, Dueker ME, Logan JR, et al (2018)

The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition.

The Science of the total environment, 647:1547-1556 pii:S0048-9697(18)33013-4 [Epub ahead of print].

Fog supplies water and nutrients to systems ranging from coastal forests to inland deserts. Fog droplets can also contain bacterial and fungal aerosols, but our understanding of fog biology is limited. Using metagenomic tools and culturing, we provide a unique look at fungal and bacterial communities in fog at two fog-dominated sites: coastal Maine (USA) and the Namib Desert (Namibia). Microbial communities in the fog at both sites were diverse, distinct from clear aerosols, and influenced by both soil and marine sources. Fog from both sites contained Actinobacteria and Firmicutes, commonly soil- and air-associated phyla, but also contained bacterial taxa associated with marine environments including Cyanobacteria, Oceanospirillales, Novosphingobium, Pseudoalteromonas, and Bradyrhizobiaceae. Marine influence on fog communities was greatest near the coast, but still evident in Namib fogs 50 km inland. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. Fog is likely to enhance viability of transported microbes and facilitate their deposition, making fog biology ecologically important in fog-dominated environments. Fog may introduce novel species to terrestrial ecosystems, including human and plant pathogens, warranting further work on the drivers of this important and underrecognized aerobiological transfer between marine and terrestrial systems.

RevDate: 2018-09-05

Urra J, Alkorta I, Mijangos I, et al (2018)

Application of sewage sludge to agricultural soil increases the abundance of antibiotic resistance genes without altering the composition of prokaryotic communities.

The Science of the total environment, 647:1410-1420 pii:S0048-9697(18)32977-2 [Epub ahead of print].

The application of sewage sludge as soil amendment is a common agricultural practice. However, wastewater treatment plants, sewage sludge and sewage sludge-amended soils have been reported as hotspots for the appearance and dissemination of antibiotic resistance, driven, among other factors, by selection pressure exerted by co-exposure to antibiotics and heavy metals. To address this threat to environmental and human health, soil samples from a long-term (24 years) field experiment, carried out to study the impact of thermally dried and anaerobically digested sewage sludge (at different doses and frequencies of application) on agricultural soil quality, were investigated for the presence of genes encoding antibiotic resistance (ARGs) and mobile genetic elements (MGEs). Sewage sludge-induced changes in specific soil physicochemical and microbial properties, as indicators of soil quality, were also investigated. The application of sewage sludge increased the total concentration of copper and zinc in amended soils, but without affecting the bioavailability of these metals, possibly due to the high values of soil pH and organic matter content. Soil microbal quality, as reflected by the value of the Soil Quality Index, was higher in sewage sludge-amended soils. Similarly, the application of sewage sludge increased soil microbial activity and biomass, as well as the abundance of ARGs and MGE genes, posing a risk of dissemination of antibiotic resistance. In contrast, the composition of soil prokaryotic communities was not significantly altered by the application of sewage sludge. We found correlation between soil Cu and Zn concentrations and the abundance of ARGs and MGE genes. It was concluded that sewage sludge-derived amendments must be properly treated and managed if they are to be applied to agricultural soil.

RevDate: 2018-09-04

Perez S, Czerner M, Patat ML, et al (2018)

Monitoring the characteristics of cultivable halophilic microbial community during salted-ripened anchovy (Engraulis anchoita) production.

International journal of food microbiology, 286:179-189 pii:S0168-1605(18)30522-1 [Epub ahead of print].

The halophilic microbial community of the salted-ripened anchovy process was studied. Samples from raw materials (salt and fresh anchovies) and from the stages of brining and ripening were collected and analyzed for their bacterial counts at 15 and 20% NaCl. No halophilic colonies were found in fresh anchovy and counts of about 103 CFU/g were determined in salt samples. A fluctuation of bacterial counts during the process was found. At the end of brining, ~104 CFU/g were determined in anchovy samples and this value was reduced to not detectable counts at the beginning of the ripening stage. After one month, counts increased to ~104 CFU/g and remained stable until the end of the process. From each sample, colonies having different morphotypes were isolated and submitted to a macro and microscopic characterization, a study of salt requirement for growth, and biochemical and phenotypic tests. The results were submitted to Univariate, Bivariate and Multiple Correspondence Factorial Analysis (MCFA). A total of 79 colonies were isolated during the salting-ripening anchovy process. Among the isolates, about 40-50% was positive for indole production and lipolytic activity and a 25% showed ability to produce H2S and proteolytic capacity. Proteolytic and lipolytic activities were well balanced along the process and resulted independent from the isolation stage, which is a desirable condition due to the contribution of microbial proteolysis and lipolysis to the development of texture and final aroma, respectively. H2S and indole producers practically were not detected during ripening. This fact is important because indole and H2S are associated with the development of off-flavors and spoilage in salted fish products. MFCA and Cluster Analyses complemented the Bivariate Analyses. The factor map showed proximity between the isolates from salt samples and from ripening. Isolates were statistically clustered in two groups. Cluster 1 grouped non-desirable activities (H2S and indole production) with cultures proceeding from brining whereas Cluster 2 related isolates mainly from salt samples and during ripening with some desirable microbial capacities (Cytochrome oxidase activity and non-H2S and non-indole production). These results would indicate that during the ripening process of salted anchovies, a natural selection of beneficial microorganisms for the development of the typical product sensory attributes occurred.

RevDate: 2018-09-04

Berube PM, Biller SJ, Hackl T, et al (2018)

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments.

Scientific data, 5:180154 pii:sdata2018154.

Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.

RevDate: 2018-09-04

Kilian M (2018)

The oral microbiome - friend or foe?.

European journal of oral sciences, 126 Suppl 1:5-12.

The microbiome and the human body constitute an integrated superorganism, which is the result of millions of years of coevolution with mutual adaptation and functional integration, and confers significant benefits for both parties. This evolutionary process has resulted in a highly diverse oral microbiome, which covers the full spectrum of acidogenic, aciduric, inflammatory, and anti-inflammatory properties. The relative proportions of members of the microbiome are affected by factors associated with modern life, such as general diet patterns, sugar consumption, tobacco smoking, oral hygiene, use of antibiotics and other antimicrobials, and vaccines. A perturbed balance in the oral microbiome may result in caries, periodontal disease, or candidiasis, and oral bacteria passively transferred to normally sterile parts of the body may cause extra-oral infections. Nevertheless, it should never be our goal to eliminate the oral microbiome, but rather we have to develop ways to re-establish a harmonious coexistence that is lost because of the modern lifestyle. With regard to oral diseases, this goal can normally be achieved by optimal oral hygiene, exposure to fluoride, reduction of sucrose consumption, stimulation of our innate immune defense, smoking cessation, and control of diabetes.

RevDate: 2018-09-04

Xu WF, Ren HS, Ou T, et al (2018)

Genomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose.

Microbial ecology pii:10.1007/s00248-018-1247-4 [Epub ahead of print].

Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 106 and 1.0 × 105 CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites. Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.

RevDate: 2018-09-03

Coenen AR, JS Weitz (2018)

Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities.

mSystems, 3(4): pii:mSystems00084-18.

Microbes are present in high abundances in the environment and in human-associated microbiomes, often exceeding 1 million per ml. Viruses of microbes are present in even higher abundances and are important in shaping microbial populations, communities, and ecosystems. Given the relative specificity of viral infection, it is essential to identify the functional linkages between viruses and their microbial hosts, particularly given dynamic changes in virus and host abundances. Multiple approaches have been proposed to infer infection networks from time series of in situ communities, among which correlation-based approaches have emerged as the de facto standard. In this work, we evaluate the accuracy of correlation-based inference methods using an in silico approach. In doing so, we compare predicted networks to actual networks to assess the self-consistency of correlation-based inference. At odds with assumptions underlying its widespread use, we find that correlation is a poor predictor of interactions in the context of viral infection and lysis of microbial hosts. The failure to predict interactions holds for methods that leverage product-moment, time-lagged, and relative-abundance-based correlations. In closing, we discuss alternative inference methods, particularly model-based methods, as a means to infer interactions in complex microbial communities with viruses. IMPORTANCE Inferring interactions from population time series is an active and ongoing area of research. It is relevant across many biological systems-particularly in virus-microbe communities, but also in gene regulatory networks, neural networks, and ecological communities broadly. Correlation-based inference-using correlations to predict interactions-is widespread. However, it is well-known that "correlation does not imply causation." Despite this, many studies apply correlation-based inference methods to experimental time series without first assessing the potential scope for accurate inference. Here, we find that several correlation-based inference methods fail to recover interactions within in silico virus-microbe communities, raising questions on their relevance when applied in situ.

RevDate: 2018-09-03

Asses N, Ayed L, Hkiri N, et al (2018)

Congo Red Decolorization and Detoxification by Aspergillus niger: Removal Mechanisms and Dye Degradation Pathway.

BioMed research international, 2018:3049686.

Congo red is one of the best known and used azo dyes which has two azo bonds (-N=N-) chromophore in its molecular structure. Its structural stability makes it highly toxic and resistant to biodegradation. The objective of this study was to assess the congo red biodegradation and detoxification by Aspergillus niger. The effects of pH, initial dye concentration, temperature, and shaking speed on the decolorization rate and enzymes production were studied. The maximum decolorization was correlated with lignin peroxidase and manganese peroxidase production. Above 97% were obtained when 2 g mycelia were incubated at pH 5, in presence of 200 mg/L of dye during 6 days at 28°C and under 120 to 150 rpm shaking speed. The degraded metabolites were characterized by using LC-MS/MS analyses and the biodegradation mechanism was also studied. Congo red bioconversion formed degradation metabolites mainly by peroxidases activities, i.e., the sodium naphthalene sulfonate (m/z = 227) and the cycloheptadienylium (m/z = 91). Phytotoxicity and microtoxicity tests confirmed that degradation metabolites were less toxic than original dye.

RevDate: 2018-09-03

Li Y, Jiang W, Gao R, et al (2018)

Fe(III)-based immobilized metal-affinity chromatography (IMAC) method for the separation of the catechol siderophore from Bacillus tequilensis CD36.

3 Biotech, 8(9):392.

Catechol siderophore plays an important role in microbial ecology, agriculture, and medicine, but its research is often limited by the difficulty in acquisition of it in large quantities. Based on evidence from the coordination chemistry and chemical biology, catechol siderophore could chelate Fe3+ with high affinity. Therefore, Fe(III)-based immobilized metal-affinity chromatography (IMAC) was applied to capture siderophore from the culture filtrate of Bacillus tequilensis CD36. The ethanol-precipitated sample and the separated sample from Fe(III)-based IMAC were analyzed by liquid chromatography-mass spectrometry. According to the result, the pure siderophore DHB-Gly-Thr could be extracted from the ethanol-precipitated sample. Compared with other purifications, Fe(III)-based IMAC was convenient and had fewer steps. In addition, it also reduced the use of toxic chemical solvents in some traditional extraction process, such as extraction and ion exchange chromatography. Fe(III)-based IMAC was successfully used in separation of the catechol siderophore from B. tequilensis CD36. The results revealed that Fe(III)-based IMAC was an efficient and environmentally friendly method for the separation and purification of catechol siderophore.

RevDate: 2018-09-02

Gänzle MG, J Zheng (2018)

Lifestyles of sourdough lactobacilli - Do they matter for microbial ecology and bread quality?.

International journal of food microbiology pii:S0168-1605(18)30542-7 [Epub ahead of print].

Sourdough is used in production of (steamed) bread as leavening agent (type I sourdoughs) or as baking improver to enhance flavour, texture, and shelf life of bread (type II sourdoughs). The long-term propagation of sourdoughs eliminates dispersal limitation and consistently leads to sourdough microbiota that are composed of host adapted lactobacilli. In contrast, community assembly in spontaneous cereal fermentations is limited by dispersal and nomadic or environmental lactic acid bacteria are the first colonizers of these sourdoughs. Propagation of sourdoughs for use as sole leavening agent (type I sourdoughs) dictates fermentation conditions that select for rapid growth. Type I wheat- and rye sourdoughs are consistently populated by insect-adapted lactobacilli, particularly Lactobacillus sanfranciscensis, which is characterized by a small genome size and a restricted metabolic potential. The diverse fermentation conditions employed in industrial or artisanal Type II sourdough fermentation processes also result in a more diverse microbiota. Nevertheless, type II sourdoughs are typically populated by vertebrate host adapted lactobacilli of the L. delbrueckii and L. reuteri groups. Metabolic traits of host-adapted lactobacilli that enhance competitiveness in intestinal ecosystems also provide technological functionality in bread making. Examples include formation of exopolysaccharides, arginine-, glutamine- and glutamate based mechanisms of acid resistance, and glycosyl hydrolases that reduce FODMAP levels in sourdough and sourdough bread. In conclusion, consideration of the lifestyle of sourdough lactobacilli facilitates the selection of competitive and functional sourdough starter cultures.

RevDate: 2018-09-01

Macintosh KA, Doody DG, Withers PJA, et al (2018)

Transforming soil phosphorus fertility management strategies to support the delivery of multiple ecosystem services from agricultural systems.

The Science of the total environment, 649:90-98 pii:S0048-9697(18)33244-3 [Epub ahead of print].

Despite greater emphasis on holistic phosphorus (P) management, current nutrient advice delivered at farm-scale still focuses almost exclusively on agricultural production. This limits our ability to address national and international strategies for the delivery of multiple ecosystem services (ES). Currently there is no operational framework in place to manage P fertility for multiple ES delivery and to identify the costs of potentially sacrificing crop yield and/or quality. As soil P fertility plays a central role in ES delivery, we argue that soil test phosphorus (STP) concentration provides a suitable common unit of measure by which delivering multiple ES can be economically valued relative to maximum potential yield, in $ ha-1 yr-1 units. This value can then be traded, or payments made against one another, at spatio-temporal scales relevant for farmer and national policy objectives. Implementation of this framework into current P fertility management strategies would allow for the integration and interaction of different stakeholder interests in ES delivery on-farm and in the wider landscape. Further progress in biophysical modeling of soil P dynamics is needed to inform its adoption across diverse landscapes.

RevDate: 2018-09-01

Szafranek-Nakonieczna A, Wolińska A, Zielenkiewicz U, et al (2018)

Activity and Identification of Methanotrophic Bacteria in Arable and No-Tillage Soils from Lublin Region (Poland).

Microbial ecology pii:10.1007/s00248-018-1248-3 [Epub ahead of print].

Methanotrophic bacteria are able to use methane (CH4) as a sole carbon and energy source. Photochemical oxidation of methane takes place in the stratosphere, whereas in the troposphere, this process is carried out by methanotrophic bacteria. On the one hand, it is known that the efficiency of biological CH4 oxidation is dependent on the mode of land use but, on the other hand, the knowledge of this impact on methanotrophic activity (MTA) is still limited. Thus, the aim of the study was to determine the CH4 oxidation ability of methanotrophic bacteria inhabiting selected arable and no-tillage soils from the Lublin region (Albic Luvisol, Brunic Arenosol, Haplic Chernozem, Calcaric Cambisol) and to identify bacteria involved in this process. MTA was determined based on incubation of soils in air with addition of methane at the concentrations of 0.002, 0.5, 1, 5, and 10%. The experiment was conducted in a temperature range of 10-30 °C. Methanotrophs in soils were identified by next-generation sequencing (NGS). MTA was confirmed in all investigated soils (in the entire range of the tested methane concentrations and temperatures, except for the arable Albic Luvisol). Importantly, the MTA values in the no-tillage soil were nearly two-fold higher than in the cultivated soils. Statistical analysis indicated a significant influence of land use, type of soil, temperature, and especially methane concentration (p < 0.05) on MTA. Metagenomic analysis confirmed the presence of methanotrophs from the genus Methylocystis (Alphaproteobacteria) in the studied soils (except for the arable Albic Luvisol). Our results also proved the ability of methanotrophic bacteria to oxidize methane although they constituted only up to 0.1% of the total bacterial community.

RevDate: 2018-08-21

Gilbert JA, B Stephens (2018)

Microbiology of the built environment.

Nature reviews. Microbiology pii:10.1038/s41579-018-0065-5 [Epub ahead of print].

The built environment comprises all structures built by humans, including our homes, workplaces, schools and vehicles. As in any ecosystem on Earth, microorganisms have been found in every part of the built environment that has been studied. They exist in the air, on surfaces and on building materials, usually dispersed by humans, animals and outdoor sources. Those microbial communities and their metabolites have been implied to cause (or exacerbate) and prevent (or mitigate) human disease. In this Review, we outline the history of the field of microbiology of the built environment and discuss recent insights that have been gained into microbial ecology, adaptation and evolution of this ecosystem. Finally, we consider the implications of this research, specifically, how it is changing the types of materials we use in buildings and how our built environments affect human health.

RevDate: 2018-08-31

Xu G, Abdullah Al M, Sikder MNA, et al (2018)

Identifying indicator redundancy of biofilm-dwelling protozoa for bioassessment in marine ecosystems.

Environmental science and pollution research international pii:10.1007/s11356-018-3063-2 [Epub ahead of print].

A multivariate peeling method of data analysis was applied to determine indicator redundancy and for identifying indicator units (IUs) among biofilm-dwelling ciliate communities used for bioassessment of marine water quality. Samples were taken monthly over a 1-year period at four stations in coastal waters of the Yellow Sea: one heavily polluted, one moderately polluted, one intermittently polluted, and one unpolluted. Four IUs (IU1-4) were identified consisting of 22, 13, 14, and 17 species, respectively, out of a total of 144 species. The IUs showed significant correlation with temporal and spatial variations in environmental variables. The redundancy levels of IUs were interchangeable in time and space. However, IU1 and IU2 generally dominated the communities in moderately and intermittently polluted areas during cool (e.g., early spring, late autumn, and winter) and warm (late spring and early autumn) seasons; IU3 dominated in warm seasons (e.g., late spring to autumn) in the heavily polluted area; and IU4 mainly dominated the samples in the unpolluted and moderately polluted areas during the late summer and early autumn. Furthermore, different trophic-functional groupings were represented within the four IUs and these were generally associated with water quality status. These findings suggest that there is high indicator redundancy in marine biofilm-dwelling ciliate communities subjected to different levels of water quality.

RevDate: 2018-08-31

Houngbédji M, Johansen P, Padonou SW, et al (2018)

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa.

Food microbiology, 76:267-278.

Mawè is a West African spontaneous fermented cereal-based dough. Different types of mawè exist varying in type of cereal and/or production condition, with fermentations lasting 24-48 h. With the aim of obtaining a comprehensive understanding of the microbial ecology of mawè processing, a microbiological characterisation was performed for four mawè types, produced at eight sites in Benin. At the onset of the fermentations lactic acid bacteria (LAB) and yeast counts were on average 7.5 ± 1.03 and 4.8 ± 0.79 Log10 cfu/g, which increased to 9.2 ± 0.38 and 7.4 ± 0.42 Log10 cfu/g, respectively, at the end of the fermentations. LAB (n = 321) and yeasts (n = 298), isolated during the fermentations, were identified. The predominant LAB and yeast species were Lactobacillus fermentum and Pichia kudriavzevii, respectively, followed by Kluyveromyces marxianus, all present throughout the mawè fermentations. Further, microbial successions took place with Weissella confusa occurring mostly at the onset, while Pediococcus acidilactici and Saccharomyces cerevisiae were mainly associated with the end of the fermentations. Species diversity was influenced both by type of cereal and production condition. The dominating strain clusters of L. fermentum and P. kudriavzevii were ubiquitous and strain diversities were influenced by type of cereal and production site.

RevDate: 2018-08-31

Eshrati M, Amadei F, Van de Wiele T, et al (2018)

Biopolymer-Based Minimal Formulations Boost Viability and Metabolic Functionality of Probiotics Lactobacillus rhamnosus GG through Gastrointestinal Passage.

Langmuir : the ACS journal of surfaces and colloids [Epub ahead of print].

The delivery of probiotic microorganisms as food additives via oral administration is a straightforward strategy to improve the intestinal microbiota. To protect probiotics from the harsh environments in the stomach and small intestine, it is necessary to formulate them in biocompatible carriers, which finally release them in the ileum and colon without losing their viability and functions. Despite major progresses in various polymer-based formulations, many of them are highly heterogeneous and too large in size and hence often "felt" by the tongue. In this study, we established a new formulation for probiotics Lactobacillus rhamnosus GG (LGG) and systematically correlated the physicochemical properties of formulations with the functions of probiotics after the delivery to different gastrointestinal compartments. By reducing the stirring speed by 1 order of magnitude during the emulsification of polyalginate in the presence of xanthan gum, we fabricated microparticles with a size well below the limit of human oral sensory systems. To improve the chemical stability, we deposited chitosan and polyalginate layers on particle surfaces and found that the deposition of a 20 nm-thick layer is already sufficient to perfectly sustain the viability of all LGG. Compared to free LGG, the colony-forming units of LGG in these formulations were by factors of 107 larger in stomach fluid and 104 larger in small intestine fluid. The metabolic functionality of LGG in polymer formulations was assessed by measuring the amount of lactate produced by LGG in a human gastrointestinal simulator, showing 5 orders of magnitude larger values compared to free LGG. The obtained results have demonstrated that the minimal formulation of LGG established here boosts not only the viability but also the metabolic functionality of probiotics throughout oral uptake, passage through the gastrointestinal tract, and delivery to the ileum and colon.

RevDate: 2018-08-30

Mackelprang R, Grube AM, Lamendella R, et al (2018)

Microbial Community Structure and Functional Potential in Cultivated and Native Tallgrass Prairie Soils of the Midwestern United States.

Frontiers in microbiology, 9:1775.

The North American prairie covered about 3.6 million-km2 of the continent prior to European contact. Only 1-2% of the original prairie remains, but the soils that developed under these prairies are some of the most productive and fertile in the world, containing over 35% of the soil carbon in the continental United States. Cultivation may alter microbial diversity and composition, influencing the metabolism of carbon, nitrogen, and other elements. Here, we explored the structure and functional potential of the soil microbiome in paired cultivated-corn (at the time of sampling) and never-cultivated native prairie soils across a three-states transect (Wisconsin, Iowa, and Kansas) using metagenomic and 16S rRNA gene sequencing and lipid analysis. At the Wisconsin site, we also sampled adjacent restored prairie and switchgrass plots. We found that agricultural practices drove differences in community composition and diversity across the transect. Microbial biomass in prairie samples was twice that of cultivated soils, but alpha diversity was higher with cultivation. Metagenome analyses revealed denitrification and starch degradation genes were abundant across all soils, as were core genes involved in response to osmotic stress, resource transport, and environmental sensing. Together, these data indicate that cultivation shifted the microbiome in consistent ways across different regions of the prairie, but also suggest that many functions are resilient to changes caused by land management practices - perhaps reflecting adaptations to conditions common to tallgrass prairie soils in the region (e.g., soil type, parent material, development under grasses, temperature and rainfall patterns, and annual freeze-thaw cycles). These findings are important for understanding the long-term consequences of land management practices to prairie soil microbial communities and their genetic potential to carry out key functions.

RevDate: 2018-08-29

Ma ZS (2018)

Sketching the Human Microbiome Biogeography with DAR (Diversity-Area Relationship) Profiles.

Microbial ecology pii:10.1007/s00248-018-1245-6 [Epub ahead of print].

SAR (species area relationship) is a classic ecological theory that has been extensively investigated and applied in the studies of global biogeography and biodiversity conservation in macro-ecology. It has also found important applications in microbial ecology in recent years thanks to the breakthroughs in metagenomic sequencing technology. Nevertheless, SAR has a serious limitation for practical applications-ignoring the species abundance and treating all species as equally abundant. This study aims to explore the biogeography discoveries of human microbiome over 18 sites of 5 major microbiome habitats, establish the baseline DAR (diversity-area scaling relationship) parameters, and perform comparisons with the classic SAR. The extension from SAR to DAR by adopting the Hill numbers as diversity measures not only overcomes the previously mentioned flaw of SAR but also allows for obtaining a series of important findings on the human microbiome biodiversity and biogeography. Specifically, two types of DAR models were built, the traditional power law (PL) and power law with exponential cutoff (PLEC), using comprehensive datasets from the HMP (human microbiome project). Furthermore, the biogeography "maps" for 18 human microbiome sites using their DAR profiles for assessing and predicting the diversity scaling across individuals, PDO profiles (pair-wise diversity overlap) for measuring diversity overlap (similarity), and MAD profile (for predicting the maximal accrual diversity in a population) were sketched out. The baseline biogeography maps for the healthy human microbiome diversity can offer guidelines for conserving human microbiome diversity and investigating the health implications of the human microbiome diversity and heterogeneity.

RevDate: 2018-08-29

Cairns J, Jokela R, Hultman J, et al (2018)

Construction and Characterization of Synthetic Bacterial Community for Experimental Ecology and Evolution.

Frontiers in genetics, 9:312.

Experimental microbial ecology and evolution have yielded foundational insights into ecological and evolutionary processes using simple microcosm setups and phenotypic assays with one- or two-species model systems. The fields are now increasingly incorporating more complex systems and exploration of the molecular basis of observations. For this purpose, simplified, manageable and well-defined multispecies model systems are required that can be easily investigated using culturing and high-throughput sequencing approaches, bridging the gap between simpler and more complex synthetic or natural systems. Here we address this need by constructing a completely synthetic 33 bacterial strain community that can be cultured in simple laboratory conditions. We provide whole-genome data for all the strains as well as metadata about genomic features and phenotypic traits that allow resolving individual strains by amplicon sequencing and facilitate a variety of envisioned mechanistic studies. We further show that a large proportion of the strains exhibit coexistence in co-culture over serial transfer for 48 days in the absence of any experimental manipulation to maintain diversity. The constructed bacterial community can be a valuable resource in future experimental work.

RevDate: 2018-08-29

Plominsky AM, Henríquez-Castillo C, Delherbe N, et al (2018)

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation.

Frontiers in microbiology, 9:1800.

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.

RevDate: 2018-08-28

Xie H, Wang H, Ji F, et al (2018)

Tetrabromobisphenol A alters soil microbial community via selective antibacterial activity.

Ecotoxicology and environmental safety, 164:597-603 pii:S0147-6513(18)30787-5 [Epub ahead of print].

Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant. Most studies regarding TBBPA have concentrated on its occurrence, distribution, toxicity and degradation in the environment. However, little is known about its ecological effects on soil microbial communities. In this study, we investigated the effect of TBBPA on soil microbial community. Overall, the data suggested that the growth and composition of soil microorganisms were correlated to the TBBPA concentration and exposure time. Phospholipid-derived fatty acid analysis (PLFAs) showed that significant microbial growth inhibitions were 46.1% and 46.9% in 40 mg/kg TBBPA-treated soils after 45-day incubation under aerobic and anaerobic conditions, respectively. Results of PLFAs and llumina sequencing indicated that TBBPA mainly inhibited Gram-positive bacteria, but not Gram-negative bacteria. The selective antibacterial activity of TBBPA toward Gram-positive bacteria was further confirmed in pure bacteria cultures. These data suggested that, in addition to their effect on microbial growth and composition, TBBPA may affect the microbial ecology. Additional research should be carried out to identify the ecological risk of TBBPA in soil.

RevDate: 2018-08-28

Vandekerckhove TGL, De Mulder C, Boon N, et al (2018)

Temperature impact on sludge yield, settleability and kinetics of three heterotrophic conversions corroborates the prospect of thermophilic biological nitrogen removal.

Bioresource technology, 269:104-112 pii:S0960-8524(18)31106-4 [Epub ahead of print].

In specific municipal and industrial cases, thermophilic wastewater treatment (>45 °C) might bring cost advantages over commonly applied mesophilic processes (10-35 °C). To develop such a novel process, one needs sound parameters on kinetics, sludge yield and sludge settleability of three heterotrophic conversions: aerobic carbon removal, denitritation and denitrification. These features were evaluated in acetate-fed sequencing batch reactors (30, 40, 50 and 60 °C). Higher temperatures were accompanied by lower sludge production and maximum specific removal rates, resulting mainly from lower maximum growth rates. Thermophilic denitritation was demonstrated for the first time, with lower sludge production (18-26%), higher nitrogen removal rates (24-92%) and lower carbon requirement (40%) compared to denitrification. Acceptable settling of thermophilic aerobic (60 °C) and anoxic biomass (50 and 60 °C) was obtained. Overall, this parameter set may catalyze the establishment of thermophilic nitrogen removal, once nitritation and nitratation are characterized. Furthermore, waters with low COD/N ratio might benefit from thermophilic nitritation/denitritation.

RevDate: 2018-08-28

Samanta A, Patra A, Mandal S, et al (2018)

Hypoxia: A cause of acute renal failure and alteration of gastrointestinal microbial ecology.

Saudi journal of kidney diseases and transplantation : an official publication of the Saudi Center for Organ Transplantation, Saudi Arabia, 29(4):879-888.

Oxygen is very important to the existence of life. Oxygen deficiency, defined as hypoxia, elicits adaptive responses in cells and tissues. Lower oxygen concentration can cause the alteration of renal function, affects the maintenance of a balance of the body fluids, electrolytes, pH, and blood pressure homeostasis. Impaired fluid regulation could, in addition, contribute to the precipitation of pulmonary edema and exacerbate hypoxemia which may accelerate the progression of chronic kidney disease. In this context, the present study attempted to evaluate the association of renal injury and oxidative stress at different atmospheric pressures (1829, 3657, and 5486 m). Limited fecal analysis of experimental animals was also done to evaluate the impact of hypobaric hypoxia on the composition of dominant gastrointestinal microbiota. The study was performed on 24 male Wister strain rats and divided into four groups (C, HA-I, HA-II, and HA-III), and exposure was carried out for seven days period. In hypoxic exposure rats, plasma urea, creatinine, electrolytes and malonaldehyde level elevated and catalase and superoxide dismutase level diminished significantly compared to the controls. Increase in blood uremia profile, toxicity markers, and lipid peroxidation marker enzymes indicated that hypoxia causes renal failure. Histological structures of the kidney of group HA-II and HA-III animals showed severe disorganization of glomerulus and dilation of renal tubules. These results indicate nephrotoxicity or acute renal failure can occur at hypobaric hypoxia and it also affected the gut microbial population. This alteration was observed significantly above 3000 m.

RevDate: 2018-08-28

Peyyala R, Emecen-Huja P, JL Ebersole (2018)

Environmental lead effects on gene expression in oral epithelial cells.

Journal of periodontal research [Epub ahead of print].

BACKGROUND AND OBJECTIVE: Host responses in periodontitis span a range of local and emigrating cell types and biomolecules. Accumulating evidence regarding the expression of this disease across the population suggests some component of genetic variation that controls onset and severity of disease, in concert with the qualitative and quantitative parameters of the oral microbiome at sites of disease. However, there remains little information regarding the capacity of accruing environmental stressors or modifiers over a lifespan at both the host genetic and microbial ecology levels to understand fully the population variation in disease. This study evaluated the impact of environmental lead exposure on the responses of oral epithelial cells to challenge with a model pathogenic oral biofilm.

METHODS AND RESULTS: Using NanoString technology to quantify gene expression profiles of an array of 511 host response-associated genes in the epithelial cells, we identified an interesting primary panel of basal responses of the cells with numerous genes not previously considered as major response markers for epithelial cells, eg, interleukin (IL)-32, CTNNB1, CD59, MIF, CD44 and CD99. Even high levels of environment lead had little effect on these constitutive responses. Challenge of the cells with the biofilms (Streptococcus gordonii/Fusobacterium nucleatum/Porphyromonas gingivalis) resulted in significant increases in an array of host immune-related genes (134 of 511). The greatest magnitude in differential expression was observed with many genes not previously described as major response genes in epithelial cells, including IL-32, CD44, NFKBIA, CTSC, TNFAIP3, IL-1A, IL-1B, IL-8 and CCL20. The effects of environmental lead on responses to the biofilms were mixed, although levels of IL-8, CCL20 and CD70 were significantly decreased at lead concentrations of 1 and/or 5 μmol/L.

CONCLUSIONS: The results provided new information on a portfolio of genes expressed by oral epithelial cells, targeted substantial increases in an array of immune-related genes post-biofilm challenge, and a focused impact of environmental lead on these induced responses.

RevDate: 2018-08-28

Szubert-Kruszyńska A, Stańczak J, Cieniuch S, et al (2018)

Bartonella and Rickettsia Infections in Haematophagous Spinturnix myoti Mites (Acari: Mesostigmata) and their Bat Host, Myotis myotis (Yangochiroptera: Vespertilionidae), from Poland.

Microbial ecology pii:10.1007/s00248-018-1246-5 [Epub ahead of print].

Hematophagous Spinturnix myoti mites and their host, the greater mouse-eared bat (Myotis myotis), were tested for the presence of Bartonella spp., Rickettsia spp., and Anaplasma phagocytophilum. In total, Bartonella spp. DNA was amplified in 28% of 134 mite pools and in 25% of 59 bats tested by PCR targeting a fragment of citrate synthase gltA gen. Adult mites were at least threefold more frequently infected compared to immature stages. The overall infection prevalence among mite pools from cave-dwelling bats was higher than for those collected from attic shelters. Three distinct genotypes were detected. The most prevalent genotype in mites and bats matched closely with Candidatus Bartonella hemsundetiensis identified in bats from Finland and was relatively distant from bat-borne Bartonella strains described in the UK and France. Importantly, most sequences were close to those reported in forest workers from Poland. The presence of identical genotype among S. myoti samples and M. myotis bats suggests that bartonellae can be shared between mites and their bat hosts. In this case, wing mites could serve as vectors, whereas their hosts as reservoirs. One blood sample was positive by PCR for the msp2 gene of A. phagocytophilum. Two mite pools yielded Rickettsia spp. DNA. Both sequences were distinct from any known species but can be classified as spotted fever group Rickettsia spp. Our findings expanded our knowledge on the role of spinturnicid mites in the ecology and epidemiology of bacterial infections associated with vespertilionid bats, especially regarding the genus Bartonella.

RevDate: 2018-08-28

Perault AI, PA Cotter (2018)

Three distinct contact-dependent growth inhibition systems mediate interbacterial competition by the cystic fibrosis pathogen Burkholderia dolosa.

Journal of bacteriology pii:JB.00428-18 [Epub ahead of print].

The respiratory tracts of individuals afflicted with cystic fibrosis (CF) harbor complex polymicrobial communities. By an unknown mechanism, species of the Gram-negative Burkholderia cepacia complex, such as Burkholderia dolosa, can displace other bacteria in the CF lung, causing cepacia syndrome, which has a poor prognosis. The genome of B. dolosa strain AU0158 (BdAU0158) contains three loci that are predicted to encode Contact-Dependent growth Inhibition (CDI) systems. CDI systems function by translocating the toxic C-terminus of a large exoprotein directly into target cells, resulting in growth inhibition or death unless the target cells produce a cognate immunity protein. We demonstrate here that each of the three bcpAIOB loci in BdAU0158 encodes a distinct CDI system that mediates interbacterial competition in an allele-specific manner. While only two of the three bcpAIOB loci are expressed under the in vitro conditions tested, the third conferred immunity under these conditions due to the presence of an internal promoter driving expression of the bcpI gene. One BdAU0158 bcpAIOB allele is highly similar to bcpAIOB in Burkholderia thailandensis strain E264 (BtE264), and we showed that their BcpI proteins are functionally interchangeable, but Contact-Dependent Signaling (CDS) phenotypes were not observed in BdAU0158. Our findings suggest that the CDI systems of BdAU0158 may provide this pathogen an ecological advantage during polymicrobial infections of the CF respiratory tract.IMPORTANCE Human-associated polymicrobial communities can promote health and disease, and interbacterial interactions influence the microbial ecology of such communities. Polymicrobial infections of the cystic fibrosis respiratory tract impair lung function and lead to death of individuals suffering from this disorder; therefore, a greater understanding of these microbial communities is necessary for improving treatment strategies. Bacteria utilize contact-dependent growth inhibition systems to kill neighboring competitors and maintain their niche within multicellular communities. Several cystic fibrosis pathogens have the potential to gain an ecological advantage during infection via contact-dependent growth inhibition systems, including Burkholderia dolosa Our research is significant as it has identified three functional contact-dependent growth inhibition systems in B. dolosa that may provide this pathogen a competitive advantage during polymicrobial infections.

RevDate: 2018-08-28

Bascuñán P, Niño-Garcia JP, Galeano-Castañeda Y, et al (2018)

Factors shaping the gut bacterial community assembly in two main Colombian malaria vectors.

Microbiome, 6(1):148 pii:10.1186/s40168-018-0528-y.

BACKGROUND: The understanding of the roles of gut bacteria in the fitness and vectorial capacity of mosquitoes that transmit malaria, is improving; however, the factors shaping the composition and structure of such bacterial communities remain elusive. In this study, a high-throughput 16S rRNA gene sequencing was conducted to understand the effect of developmental stage, feeding status, species, and geography on the composition of the gut bacterial microbiota of two main Colombian malaria vectors, Anopheles nuneztovari and Anopheles darlingi.

RESULTS: The results revealed that mosquito developmental stage, followed by geographical location, are more important determinants of the gut bacterial composition than mosquito species or adult feeding status. Further, they showed that mosquito gut is a major filter for environmental bacteria colonization.

CONCLUSIONS: The sampling design and analytical approach of this study allowed to untangle the influence of factors that are simultaneously shaping the microbiota composition of two Latin-American malaria vectors, essential aspect for the design of vector biocontrol strategies.

RevDate: 2018-08-27

Papathanasiou P, Erdmann S, Leon-Sobrino C, et al (2018)

Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1.

RNA biology [Epub ahead of print].

Carrier state viral infection constitutes an equilibrium state in which a limited fraction of a cellular population is infected while the remaining cells are transiently resistant to infection. This type of infection has been characterized for several bacteriophages but not, to date, for archaeal viruses. Here we demonstrate that the rudivirus SIRV3 can produce a host-dependent carrier state infection in the model crenarchaeon Sulfolobus. SIRV3 only infected a fraction of a Sulfolobus islandicus REY15A culture over several days during which host growth was unimpaired and no chromosomal DNA degradation was observed. CRISPR-Cas spacer acquisition from SIRV3 DNA was induced by coinfecting with the bicaudavirus SMV1 and it was coincident with increased transcript levels from subtype I-A adaptation and interference cas genes. However, this response did not significantly affect the carrier state infection of SIRV3 and both viruses were maintained in the culture over 12 days during which SIRV3 anti-CRISPR genes were shown to be expressed. Transcriptome and proteome analyses demonstrated that most SIRV3 genes were expressed at varying levels over time whereas SMV1 gene expression was generally low. The study yields insights into the basis for the stable infection of SIRV3 and the resistance to the different host CRISPR-Cas interference mechanisms. It also provides a rationale for the commonly observed coinfection of archaeal cells by different viruses in natural environments.

RevDate: 2018-08-26

Daghio M, Vaiopoulou E, Aulenta F, et al (2018)

Anode potential selection for sulfide removal in contaminated marine sediments.

Journal of hazardous materials, 360:498-503 pii:S0304-3894(18)30694-0 [Epub ahead of print].

Sulfate reducing microorganisms are typically involved in hydrocarbon biodegradation in the sea sediment, with their metabolism resulting in the by-production of toxic sulfide. In this context, it is of utmost importance identifying the optimal value for anodic potential which ensures efficient toxic sulfide removal. Along this line, in this study the (bio)electrochemical removal of sulfide was tested at anodic potentials of -205 mV, +195 mV and +300 mV (vs Ag/AgCl), also in the presence of a pure culture of the sulfur-oxidizing bacterium Desulfobulbus propionicus. Current production, sulfide concentration and sulfate concentration were monitored over time. At the end of the experiment sulfur deposition on the electrodes and the microbial communities were characterized by SEM-EDS and by next generation sequencing of the 16S rRNA gene respectively. Results confirmed that current production was linked to sulfide removal and D. propionicus promoted back oxidation of deposited sulfur to sulfate. The highest electron recovery was observed at +195 mV vs Ag/AgCl, and the lowest sulfur deposition was obtained at -205 mV vs Ag/AgCl anode polarization.

RevDate: 2018-08-26

Chen L, Xu W, Lee A, et al (2018)

The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: An open-label, randomized clinical trial.

EBioMedicine pii:S2352-3964(18)30318-9 [Epub ahead of print].

BACKGROUND: Helicobacter pylori (H. pylori) infection is associated with remodeling of gastric microbiota. However, comprehensive analyses of the impact of H. pylori infection, eradication therapy and probiotic supplementation on gut microbiota are still lacking. We aimed to provide evidence for clinical decision making.

METHODS: Seventy H. pylori-positive and 35 H. pylori-negative patients (group C) were enrolled. H. pylori-positive patients were randomly assigned to group A (14-day bismuth-containing quadruple therapy) and group B (quadruple therapy supplemented with Clostridium butyricum). Stool samples of group A and B were collected on day 0, 14 and 56 while stool samples of group C were collected on day 0. Gut microbiota was investigated by 16S rRNA sequencing.

FINDINGS: The Sobs index (richness estimator) was significantly higher in H. pylori-positive samples than H. pylori-negative samples (p < .05). Several metabolic pathways were more abundant in H. pylori-positive communities while some disease-associated pathways had higher potential in H. pylori-negative community through KEGG pathway analysis. Abundances of most butyrate-producing bacteria significantly decreased, while several detrimental bacteria increased after eradication therapy. Probiotic supplementation was associated with improved gastrointestinal symptoms as well as increased Bacteroidetes:Firmicutes ratio.

INTERPRETATION: While H. pylori infection may not be necessarily detrimental in all patients, eradication of H. pylori was associated with widespread changes in gut microbial ecology and structure. Probiotic supplementation could relieve more gastrointestinal symptoms by inducing alterations in gut microbiota and host immune responses. As such, the decision to eradicate H. pylori should be based on comprehensive analysis of individual patients.

RevDate: 2018-08-25

Hall EK, Bernhardt ES, Bier RL, et al (2018)

Understanding how microbiomes influence the systems they inhabit.

Nature microbiology, 3(9):977-982.

Translating the ever-increasing wealth of information on microbiomes (environment, host or built environment) to advance our understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes that they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. We propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level processes of interest. Here, we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system-level processes that they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted using constituent taxa (community-aggregated traits) from those properties that cannot currently be predicted using constituent taxa (emergent properties). Existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these three categories of microbial characteristics and connect them with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance discovery and understanding across a broad range of microbiome science.

RevDate: 2018-08-25

Benicio LM, Simionato AS, Novello CR, et al (2018)

RNAm expression profile of cancer marker genes in HepG2 cells treated with different concentrations of a new indolin-3-one from Pseudomonas aeruginosa.

Scientific reports, 8(1):12781 pii:10.1038/s41598-018-30893-w.

The present study tested the effects of a newly identified indolin-3-one compound (compound 1), produced by Pseudomonas aeruginosa, on HepG2 cells. The MTT assays demonstrated decreased metabolic activities in HepG2 cells treated with compound 1, with dose- and time-dependent intensifying effect, starting at a concentration of 40 µM. The IC50 after 24, 48, 72, and 96 h treatments were 41.35, 52.7, 92.79 and 66.65 μM of compound 1, respectively. Below 80 µM, no significative damage on erythrocytes membranes was observed by the hemolytic assays. The RT-qPCR revealed that the compound modulated key genes involved in carcinogenesis process, indicating possible indolin-3-one mechanisms of action. The data showed that gene expression alterations promoted by compound 1, in concentrations up to 60 μM after 48 h, led to a decrease in cellular progression and there was no direct cellular damage. In addition, non-cytotoxic concentrations of compound 1 halved the concentration of the chemotherapeutic doxorubicin, maintaining similar therapeutic effect against HepG2 cells. The novelty of the molecule and the biological activities observed in the present study emphasize the potential of the compound 1 in cancer therapy research.

RevDate: 2018-08-24

Pace NR (2018)

The small things can matter.

PLoS biology, 16(8):e3000009 pii:PBIOLOGY-D-18-00287 [Epub ahead of print].

In the context of biology as a whole and of our own personal lives, seemingly small things can prove surprisingly influential. Here, I consider the powerful impact of small organisms-the inhabitants of the microbial world-and the small events that shaped my own development as a scientist. I reflect on the early days of the fields of molecular biology and microbial ecology and my own role in the origin story of what we now call "metagenomics".

RevDate: 2018-08-24

Li H, Mishra M, Ding S, et al (2018)

Diversity and Dynamics of "Candidatus Endobugula" and Other Symbiotic Bacteria in Chinese Populations of the Bryozoan, Bugula neritina.

Microbial ecology pii:10.1007/s00248-018-1233-x [Epub ahead of print].

Bugula neritina is a common invasive cosmopolitan bryozoan that harbors (like many sessile marine invertebrates) a symbiotic bacterial (SB) community. Among the SB of B. neritina, "Candidatus Endobugula sertula" continues to receive the greatest attention, because it is the source of bryostatins. The bryostatins are potent bioactive polyketides, which have been investigated for their therapeutic potential to treat various cancers, Alzheimer's disease, and AIDS. In this study, we compare the metagenomics sequences for the 16S ribosomal RNA gene of the SB communities from different geographic and life cycle samples of Chinese B. neritina. Using a variety of approaches for estimating alpha/beta diversity and taxonomic abundance, we find that the SB communities vary geographically with invertebrate and fish mariculture and with latitude and environmental temperature. During the B. neritina life cycle, we find that the diversity and taxonomic abundances of the SB communities change with the onset of host metamorphosis, filter feeding, colony formation, reproduction, and increased bryostatin production. "Ca. Endobugula sertula" is confirmed as the symbiont of the Chinese "Ca. Endobugula"/B. neritina symbiosis. Our study extends our knowledge about B. neritina symbiosis from the New to the Old World and offers new insights into the environmental and life cycle factors that can influence its SB communities, "Ca. Endobugula," and bryostatins more globally.

RevDate: 2018-08-24

Choi Y, Banerjee A, McNish S, et al (2018)

Co-occurrence of Anaerobes in Human Chronic Wounds.

Microbial ecology pii:10.1007/s00248-018-1231-z [Epub ahead of print].

Chronic wounds are wounds that have failed to heal after 3 months of appropriate wound care. Previous reports have identified a diverse collection of bacteria in chronic wounds, and it has been postulated that bacterial profile may contribute to delayed healing. The purpose of this study was to perform a microbiome assessment of the Wound Healing and Etiology (WE-HEAL) Study cohort, including underlying comorbidities less commonly studied in the context of chronic wounds, such as autoimmune diseases, and investigate possible relationships of the wound microbiota with clinical healing trends. We examined chronic wound specimens from 60 patients collected through the WE-HEAL Study using 16S ribosomal RNA gene sequencing. A group of co-occurring obligate anaerobes was identified from taxonomic analysis guided by Dirichlet multinomial mixtures (DMM) modeling. The group includes members of the Gram-positive anaerobic cocci (GPAC) of the Clostridia class (i.e., Anaerococcus, Finegoldia, and Peptoniphilus) and additional strict anaerobes (i.e., Porphyromonas and Prevotella). We showed that the co-occurring group of obligate anaerobes not only co-exists with commonly identified wound species (such as Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas, Corynebacterium, and Streptococcus), but importantly, they could also predominate the wound microbiota. Furthermore, examination of clinical comorbidities of the WE-HEAL specimens showed that specific obligate and facultative anaerobes were significantly reduced in wounds presented with autoimmune disease. With respect to future healing trends, no association with the wound microbiome community or the abundance of individual wound species could be established. In conclusion, we identified a co-occurring obligate anaerobic community type that predominated some human chronic wounds and underrepresentation of anaerobes in wounds associated with autoimmune diseases. Possible elucidation of host environments or key factors that influence anaerobe colonization warrants further investigation in a larger cohort.

RevDate: 2018-08-23

Zeineldin M, Barakat R, Elolimy A, et al (2018)

Synergetic action between the rumen microbiota and bovine health.

Microbial pathogenesis pii:S0882-4010(18)30982-3 [Epub ahead of print].

Host-rumen-microbe interactions are an essential component of many physiological processes, and therefore can affect ruminant health. Classical knowledge of rumen microbiology is based on culture-dependent methodologies, which only account for 10-20% of the rumen bacterial communities. While, the advancement in DNA sequencing and bioinformatics platforms provide novel approaches to investigate the composition and dynamics of the rumen microbiome. Recent studies demonstrated that the ruminal ecosystem is highly diverse and harbors numerous microbial communities. The composition of these microbial communities is affected by various environmental factors such as nutrition and different management strategies. Disturbance in the microbial ecology of the rumen is associated with the development of various diseases. Despite the flow of recent rumen-based studies, rumen microbiome is still not fully characterized. This review provides an overview of recent efforts to characterize rumen microbiome and its potential role in rumen health and disease. Moreover, the recent effects of dietary interventions and probiotics on rumen microbiome are discussed.

RevDate: 2018-08-23

Lekeux G, Laurent C, Joris M, et al (2018)

di-Cysteine motifs in the C-terminus of plant HMA4 proteins confer nanomolar affinity for zinc and are essential for HMA4 function in vivo.

Journal of experimental botany pii:5077935 [Epub ahead of print].

The PIB ATPase Heavy Metal ATPase 4 (HMA4) has a central role in the zinc homeostasis network of Arabidopsis thaliana. This membrane protein loads metal from the pericycle cells into the xylem in roots, thereby allowing root to shoot metal translocation. Moreover, HMA4 is key for zinc hyperaccumulation as well as zinc and cadmium hypertolerance in the pseudometallophyte Arabidopsis halleri. The plant-specific cytosolic C-terminal extension of HMA4 is rich in putative metal-binding residues and substantially diverged between A. thaliana and A. halleri. To clarify the function of the domain in both species, protein variants with truncated C-terminal extension, as well as with mutated di-Cys motifs and/or a His-stretch, were functionally characterized. We show that di-Cys motifs, but not the His-stretch, contribute to high affinity zinc binding and function in planta. We suggest that the HMA4 C-terminal extension is at least partly responsible for protein targeting to the plasma membrane. Finally, we reveal that the C-terminal extensions of both A. thaliana and A. halleri HMA4 proteins share similar function, despite marginally different zinc-binding capacity.

RevDate: 2018-08-23

Luk AW, Beckmann S, M Manefield (2018)

Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater.

FEMS microbiology ecology, 94(10):.

Quantification of microbes in water systems is essential to industrial practices ranging from drinking water and wastewater treatment to groundwater remediation. While quantification using DNA-based molecular methods is precise, the accuracy is dependent on DNA extraction efficiencies. We show that the DNA yield is strongly impacted by the cell concentration in groundwater samples (r = -0.92, P < 0.0001). This has major implications for industrial applications using quantitative polymerase chain reaction (qPCR) to determine cell concentrations in water, including bioremediation. We propose a simple normalization method using a DNA recovery ratio, calculated with the total cell count and DNA yield. Application of this method to enumeration of bacteria and archaea in groundwater samples targeting phylogenetic markers (16S rRNA) demonstrated an increased goodness of fit after normalization (7.04 vs 0.94 difference in Akaike's information criteria). Furthermore, normalization was applied to qPCR quantification of functional genes and combined with DNA sequencing of archaeal and bacterial 16S rRNA genes to monitor changes in abundance of methanogenic archaea and sulphate-reducing bacteria in groundwater. The integration of qPCR and DNA sequencing with appropriate normalization enables high-throughput quantification of microbial groups using increasingly affordable and accessible techniques. This research has implications for microbial ecology and engineering research as well as industrial practice.

RevDate: 2018-08-23

Geesink P, Tyc O, Küsel K, et al (2018)

Growth promotion and inhibition induced by interactions of groundwater bacteria.

FEMS microbiology ecology pii:5076029 [Epub ahead of print].

Microorganisms can produce a plethora of secondary metabolites, some acting as signaling compounds, and others as suppressing agents. As yet, the potential of groundwater microbes to produce antimicrobial compounds to increase their competitiveness against other bacteria has not been examined. In this study, we developed an AlamarBlue® based high-throughput screening method that allowed for a fast and highly standardized evaluation of both growth inhibiting and promoting metabolites. With this technique, 149 screened bacterial isolates were grown in monocultures and in 1402 co-cultures. Co-cultivation did not increase the frequency of growth inhibition against the two tested model organisms (S. aureus 533R4 and E. coli WA321) compared to monocultures. Mainly co-cultivation of Proteobacteria induced growth inhibition of both model organisms. Only slightly increased growth promotion of S. aureus 533R4 was observed. Growth promoting effects on E. coli WA321 were observed by supernatants from co-cultures between Bacteroidetes and Firmicutes. With the standardized screening for both, growth inhibiting and promoting effects, this method will enable further studies to elaborate and better understand complex interspecific interactions and networks in aquatic communities as well as in other environments.

RevDate: 2018-08-23

Vikström K, J Wikner (2018)

Importance of Bacterial Maintenance Respiration in a Subarctic Estuary: a Proof of Concept from the Field.

Microbial ecology pii:10.1007/s00248-018-1244-7 [Epub ahead of print].

Bacterial respiration contributes to atmospheric carbon dioxide accumulation and development of hypoxia and is a critical, often overlooked, component of ecosystem function. This study investigates the concept that maintenance respiration is a significant proportion of bacterial respiration at natural nutrient levels in the field, advancing our understanding of bacterial living conditions and energy strategies. Two river-sea transects of respiration and specific growth rates were analyzed representing low- and high-productivity conditions (by in situ bacterial biomass production) in a subarctic estuary, using an established ecophysiological linear model (the Pirt model) estimating maintenance respiration. The Pirt model was applicable to field conditions during high, but not low, bacterial biomass production. However, a quadratic model provided a better fit to observed data, accounting for the maintained respiration at low μ. A first estimate of maintenance respiration was 0.58 fmol O2 day-1 cell-1 by the quadratic model. Twenty percent to nearly all of the bacterial respiration was due to maintenance respiration over the observed range of μ (0.21-0.002 day-1). In the less productive condition, bacterial specific respiration was high and without dependence on μ, suggesting enhanced bacterial energy expenditure during starvation. Annual maintenance respiration accounted for 58% of the total bacterioplankton respiration based on μ from monitoring data. Phosphorus availability occasionally, but inconsistently, explained some of the remaining variation in bacterial specific respiration. Bacterial maintenance respiration can constitute a large share of pelagic respiration and merit further study to understand bacterial energetics and oxygen dynamics in the aquatic environment.

RevDate: 2018-08-22

Seugendo M, Janssen I, Lang V, et al (2018)

Prevalence and Strain Characterization of Clostridioides (Clostridium) difficile in Representative Regions of Germany, Ghana, Tanzania and Indonesia - A Comparative Multi-Center Cross-Sectional Study.

Frontiers in microbiology, 9:1843.

Clostridioides (Clostridium) difficile infections (CDI) are considered worldwide as emerging health threat. Uptake of C. difficile spores may result in asymptomatic carrier status or lead to CDI that could range from mild diarrhea, eventually developing into pseudomembranous colitis up to a toxic megacolon that often results in high mortality. Most epidemiological studies to date have been performed in middle- and high income countries. Beside others, the use of antibiotics and the composition of the microbiome have been identified as major risk factors for the development of CDI. We therefore postulate that prevalence rates of CDI and the distribution of C. difficile strains differ between geographical regions depending on the regional use of antibiotics and food habits. A total of 593 healthy control individuals and 608 patients suffering from diarrhea in communities in Germany, Ghana, Tanzania and Indonesia were selected for a comparative multi-center cross-sectional study. The study populations were screened for the presence of C. difficile in stool samples. Cultured C. difficile strains (n = 84) were further subtyped and characterized using PCR-ribotyping, determination of toxin production, and antibiotic susceptibility testing. Prevalence rates of C. difficile varied widely between the countries. Whereas high prevalence rates were observed in symptomatic patients living in Germany and Indonesia (24.0 and 14.7%), patients from Ghana and Tanzania showed low detection rates (4.5 and 6.4%). Differences were also obvious for ribotype distribution and toxin repertoires. Toxin A+/B+ ribotypes 001/072 and 078 predominated in Germany, whereas most strains isolated from Indonesian patients belonged to toxin A+/B+ ribotype SLO160 and toxin A-/B+ ribotype 017. With 42.9-73.3%, non-toxigenic strains were most abundant in Africa, but were also found in Indonesia at a rate of 18.2%. All isolates were susceptible to vancomycin and metronidazole. Mirroring the antibiotic use, however, moxifloxacin resistance was absent in African C. difficile isolates but present in Indonesian (24.2%) and German ones (65.5%). This study showed that CDI is a global health threat with geographically different prevalence rates which might reflect distinct use of antibiotics. Significant differences for distributions of ribotypes, toxin production, and antibiotic susceptibilities were observed.

RevDate: 2018-08-21

Wallace J, Laforest-Lapointe I, SW Kembel (2018)

Variation in the leaf and root microbiome of sugar maple (Acer saccharum) at an elevational range limit.

PeerJ, 6:e5293 pii:5293.

Background: Bacteria, archaea, viruses and fungi live in various plant compartments including leaves and roots. These plant-associated microbial communities have many effects on host fitness and function. Global climate change is impacting plant species distributions, a phenomenon that will affect plant-microbe interactions both directly and indirectly. In order to predict plant responses to global climate change, it will be crucial to improve our understanding of plant-microbe interactions within and at the edge of plant species natural ranges. While microbes affect their hosts, in turn the plant's attributes and the surrounding environment drive the structure and assembly of the microbial communities themselves. However, the patterns and dynamics of these interactions and their causes are poorly understood.

Methods: In this study, we quantified the microbial communities of the leaves and roots of seedlings of the deciduous tree species sugar maple (Acer saccharum Marshall) within its natural range and at the species' elevational range limit at Mont-Mégantic, Quebec. Using high-throughput DNA sequencing, we quantified the bacterial and fungal community structure in four plant compartments: the epiphytes and endophytes of leaves and roots. We also quantified endophytic fungal communities in roots.

Results: The bacterial and fungal communities of A. saccharum seedlings differ across elevational range limits for all four plant compartments. Distinct microbial communities colonize each compartment, although the microbial communities inside a plant's structure (endophytes) were found to be a subset of the communities found outside the plant's structure (epiphytes). Plant-associated bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes while the main fungal taxa present were Ascomycota.

Discussion: We demonstrate that microbial communities associated with sugar maple seedlings at the edge of the species' elevational range differ from those within the natural range. Variation in microbial communities differed among plant components, suggesting the importance of each compartment's exposure to changes in biotic and abiotic conditions in determining variability in community structure. These findings provide a greater understanding of the ecological processes driving the structure and diversity of plant-associated microbial communities within and at the edge of a plant species range, and suggest the potential for biotic interactions between plants and their associated microbiota to influence the dynamics of plant range edge boundaries and responses to global change.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
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Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )